Merge branch 'galaxyproject:main' into bwoutzerosept30

galaxyproject · Sep 30, 2024 · 6eea952 · 6eea952
2 parents e0d1157 + 03fbb13
commit 6eea952
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Showing 18 changed files with 43 additions and 46 deletions.
diff --git a/tool_collections/snpeff/.lint_skip b/tool_collections/snpeff/.lint_skip
diff --git a/tool_collections/snpeff/snpEff.xml b/tool_collections/snpeff/snpEff.xml
@@ -159,9 +159,6 @@
             </when>
             <when value="history">
                 <param name="snpeff_db" type="data" format="snpeffdb" label="@SNPEFF_VERSION@ Genome Data">
-                    <options options_filter_attribute="metadata.snpeff_version" >
-                        <filter type="add_value" value="@SNPEFF_VERSION@" />
-                    </options>
                     <validator type="expression" message="This version of SnpEff will only work with @SNPEFF_VERSION@ genome databases">value is not None and value.metadata.snpeff_version == "@SNPEFF_VERSION@"</validator>
                 </param>
                 <section name="reg_section" expanded="false" title="Regulation options">
@@ -181,9 +178,6 @@
             </when>
             <when value="custom">
                 <param name="snpeff_db" type="data" format="snpeffdb" label="@SNPEFF_VERSION@ Genome Data">
-                    <options options_filter_attribute="metadata.snpeff_version" >
-                        <filter type="add_value" value="@SNPEFF_VERSION@" />
-                    </options>
                     <validator type="expression" message="This version of SnpEff will only work with @SNPEFF_VERSION@ genome databases">value is not None and value.metadata.snpeff_version == "@SNPEFF_VERSION@"</validator>
                 </param>
                 <param name="codon_table" type="select" label="Select genetic code for this sequence" help="If this sequence uses non-standard genetic code, select one from these options">
@@ -364,30 +358,35 @@
             </change_format>
         </data>
         <data name="statsFile" format="html" label="${tool.name} on ${on_string} - HTML stats">
-            <filter>generate_stats == True</filter>
+            <filter>generate_stats</filter>
         </data>
         <data name="csvFile" format="csv" label="${tool.name} on ${on_string} - CSV stats">
-            <filter>csvStats == True</filter>
+            <filter>csvStats</filter>
         </data>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="2">
             <param name="input" ftype="vcf" value="input.vcf"/>
             <param name="inputFormat" value="vcf"/>
             <param name="outputFormat" value="vcf"/>
             <param name="genomeSrc" value="named"/>
             <param name="genome_version" value="ebola_zaire"/>
             <param name="udLength" value="0"/>
-            <param name="generate_stats" value="false"/>
+            <param name="generate_stats" value="true"/>
             <output name="snpeff_output">
                 <assert_contents>
                     <has_text_matching expression="KJ660346\t572\t.*missense_variant" />
                     <has_text_matching expression="KJ660346\t1024\t.*synonymous_variant" />
                 </assert_contents>
             </output>
+            <output name="statsFile">
+                <assert_contents>
+                    <has_text text="&lt;b&gt;"/>
+                </assert_contents>
+            </output>
         </test>
         <!-- Test interval option-->
-        <test>
+        <test expect_num_outputs="2">
             <param name="input" ftype="vcf" value="input.vcf"/>
             <param name="inputFormat" value="vcf"/>
             <param name="outputFormat" value="vcf"/>
@@ -396,12 +395,19 @@
             <param name="genome_version" value="ebola_zaire"/>
             <param name="udLength" value="0"/>
             <param name="generate_stats" value="false"/>
+            <param name="csvStats" value="true"/>
             <output name="snpeff_output">
                 <assert_contents>
                     <has_text_matching expression="KJ660346\t572\t.*missense_variant" />
                     <has_text_matching expression="KJ660346\t1024\t.*synonymous_variant" />
                 </assert_contents>
             </output>
+            <output name="csvFile">
+                <assert_contents>
+                    <has_n_lines n="185"/>
+                    <has_n_columns n="1" sep=","/>
+                </assert_contents>
+            </output>
         </test>
     </tests>
     <help><![CDATA[

diff --git a/tool_collections/snpeff/snpEff_create_db.xml b/tool_collections/snpeff/snpEff_create_db.xml
@@ -124,7 +124,7 @@
         </data>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="2">
             <param name="genome_version" value="pBR322"/>
             <param name="input_type_selector" value="gb"/>
             <param name="input" value="pBR322.gbk" />
@@ -135,7 +135,7 @@
             </output>
             <output name="output_fasta" value="pBR322_test1.fna"/>
         </test>
-        <test>
+        <test expect_num_outputs="2">
             <param name="genome_version" value="pBR322"/>
             <param name="input_type_selector" value="gb"/>
             <param name="input" value="pBR322.gbk.gz" />
@@ -146,7 +146,7 @@
             </output>
             <output name="output_fasta" value="pBR322_test1.fna"/>
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <param name="genome_version" value="pBR322"/>
             <param name="input_type_selector" value="gff"/>
             <param name="reference_source_selector" value="history"/>
@@ -158,7 +158,7 @@
                 </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <param name="genome_version" value="pBR322"/>
             <param name="input_type_selector" value="gff"/>
             <param name="reference_source_selector" value="history"/>
@@ -170,7 +170,7 @@
                 </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <param name="genome_version" value="Saccharomyces_mito"/>
             <param name="input_type_selector" value="gtf"/>
             <param name="reference_source_selector" value="history"/>

diff --git a/tool_collections/snpeff/snpeff_get_chr_names.xml b/tool_collections/snpeff/snpeff_get_chr_names.xml
@@ -50,9 +50,6 @@
             <when value="history">
                 <param name="snpeff_db" type="data" format="snpeffdb" label="@SNPEFF_VERSION@ Genome Data">
                     <help>This can only be used on databases in your history that were downloaded using the snpEff download tool.</help>
-                    <options options_filter_attribute="metadata.snpeff_version" >
-                        <filter type="add_value" value="@SNPEFF_VERSION@" />
-                    </options>
                     <validator type="expression" message="This version of SnpEff will only work with @SNPEFF_VERSION@ genome databases">value is not None and value.metadata.snpeff_version == "@SNPEFF_VERSION@"</validator>
                 </param>
             </when>
@@ -65,9 +62,6 @@
             <when value="custom">
                 <param name="snpeff_db" type="data" format="snpeffdb" label="@SNPEFF_VERSION@ Genome Data">
                     <help>This can only be used on databases in your history that were created using the snpEff build tool.</help>
-                    <options options_filter_attribute="metadata.snpeff_version" >
-                        <filter type="add_value" value="@SNPEFF_VERSION@" />
-                    </options>
                     <validator type="expression" message="This version of SnpEff will only work with @SNPEFF_VERSION@ genome databases">value is not None and value.metadata.snpeff_version == "@SNPEFF_VERSION@"</validator>
                 </param>
             </when>

diff --git a/tools/gtdbtk/gtdbtk_classify_wf.xml b/tools/gtdbtk/gtdbtk_classify_wf.xml
@@ -39,7 +39,7 @@ $advanced.force
         <param name="input" type="data" format="fasta,fasta.gz" multiple="true" label="Fasta (Genome) files"/>
         <param name="gtdbtk_db" type="select" label="GTDB-Tk database" help="This version of GTDB-Tk requires GTDB version 207 or 214. Please contact your service administrator if this version is not available to select.">
             <options from_data_table="gtdbtk_database_versioned">
-                <filter type="regexp" column="version" value="^2(07|14)$"/>
+                <filter type="regexp" column="version" value="^220$"/>
                 <validator type="no_options" message="No locally cached GTDB-Tk database is available"/>
             </options>
         </param>

diff --git a/tools/gtdbtk/macros.xml b/tools/gtdbtk/macros.xml
@@ -1,6 +1,6 @@
 <macros>
-    <token name="@TOOL_VERSION@">2.3.2</token>
-    <token name="@VERSION_SUFFIX@">5</token>
+    <token name="@TOOL_VERSION@">2.4.0</token>
+    <token name="@VERSION_SUFFIX@">0</token>
     <token name="@PROFILE@">22.05</token>
     <xml name="requirements">
         <requirements>

diff --git a/tools/sinto/macros.xml b/tools/sinto/macros.xml
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <macros>
-    <token name="@TOOL_VERSION@">0.9.0</token>
-    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@TOOL_VERSION@">0.10.1</token>
+    <token name="@VERSION_SUFFIX@">0</token>
 
     <xml name="citations">
         <citations>

diff --git a/tools/tn93/macros.xml b/tools/tn93/macros.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <macros>
-    <token name="@TOOL_VERSION@">1.0.6</token>
+    <token name="@TOOL_VERSION@">1.0.14</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">tn93</requirement>

diff --git a/tools/tn93/readreduce.xml b/tools/tn93/readreduce.xml
@@ -1,4 +1,4 @@
-<tool id="tn93_readreduce" name="Merge matching reads" version="@TOOL_VERSION@+galaxy1">
+<tool id="tn93_readreduce" name="Merge matching reads" version="@TOOL_VERSION@+galaxy0">
     <description>into clusters with TN-93</description>
     <macros>
         <import>macros.xml</import>

diff --git a/tools/tn93/tn93.xml b/tools/tn93/tn93.xml
@@ -1,4 +1,4 @@
-<tool id="tn93" name="TN93" version="@TOOL_VERSION@+galaxy1">
+<tool id="tn93" name="TN93" version="@TOOL_VERSION@+galaxy0">
     <description>compute distances between aligned sequences</description>
     <macros>
         <import>macros.xml</import>

diff --git a/tools/tn93/tn93_cluster.xml b/tools/tn93/tn93_cluster.xml
@@ -1,4 +1,4 @@
-<tool id="tn93_cluster" name="TN93 Cluster" version="@TOOL_VERSION@+galaxy1">
+<tool id="tn93_cluster" name="TN93 Cluster" version="@TOOL_VERSION@+galaxy0">
     <description>sequences that lie within a specific distance of each other</description>
     <macros>
         <import>macros.xml</import>

diff --git a/tools/tn93/tn93_filter.xml b/tools/tn93/tn93_filter.xml
@@ -1,10 +1,10 @@
-<tool id="tn93_filter" name="TN93 Filter" version="@TOOL_VERSION@+galaxy1">
+<tool id="tn93_filter" name="TN93 Filter" version="@TOOL_VERSION@+galaxy0">
     <description>- remove sequences from a reference that are within a given distance of of a cluster</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements">
-        <requirement type="package" version="1.70">biopython</requirement>
+        <requirement type="package" version="1.84">biopython</requirement>
     </expand>
     <version_command><![CDATA[tn93 --version]]></version_command>
     <command detect_errors="exit_code"><![CDATA[

diff --git a/tools/tximport/tximport.xml b/tools/tximport/tximport.xml
@@ -1,6 +1,6 @@
 <tool id="tximport" name="tximport" version="@TOOL_VERSION@" profile="20.09">
     <macros>
-        <token name="@TOOL_VERSION@">1.22.0</token>
+        <token name="@TOOL_VERSION@">1.30.0</token>
     </macros>
     <description>Summarize transcript-level estimates for gene-level analysis</description>
     <xrefs>
@@ -9,8 +9,8 @@
     </xrefs>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">bioconductor-tximport</requirement>
-        <requirement type="package" version="1.46.1">bioconductor-genomicfeatures</requirement>
-        <requirement type="package" version="1.20.3">r-getopt</requirement>
+        <requirement type="package" version="1.54.1">bioconductor-genomicfeatures</requirement>
+        <requirement type="package" version="1.20.4">r-getopt</requirement>
     </requirements>
 
     <stdio>

diff --git a/tools/ucsc_blat/blat.xml b/tools/ucsc_blat/blat.xml
@@ -1,8 +1,8 @@
 <tool id="ucsc_blat" name="UCSC BLAT Alignment Tool" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
     <description>BLAST-like sequence alignment tool</description>
     <macros>
-        <token name="@TOOL_VERSION@">377</token>
-        <token name="@VERSION_SUFFIX@">2</token>
+        <token name="@TOOL_VERSION@">469</token>
+        <token name="@VERSION_SUFFIX@">0</token>
 
         <xml name="mask_cond" tokens="maskarg,label,help">
             <conditional name="@MASKARG@_type">

diff --git a/tools/ucsc_tools/ucsc_chainsort/chainsort.xml b/tools/ucsc_tools/ucsc_chainsort/chainsort.xml
@@ -3,7 +3,7 @@
         Sort chains
     </description>
     <macros>
-        <token name="@TOOL_VERSION@">455</token>
+        <token name="@TOOL_VERSION@">469</token>
     </macros>
     <xrefs>
         <xref type="bio.tools">UCSC_Genome_Browser_Utilities</xref>

diff --git a/tools/umi_tools/macros.xml b/tools/umi_tools/macros.xml
@@ -3,8 +3,8 @@
 
     <!-- macros applying to all umi_tools -->
 
-    <token name="@TOOL_VERSION@">1.1.2</token>
-    <token name="@VERSION_SUFFIX@">2</token>
+    <token name="@TOOL_VERSION@">1.1.5</token>
+    <token name="@VERSION_SUFFIX@">0</token>
     <token name="@PROFILE@">21.01</token>
     <xml name="requirements">
         <requirements>

diff --git a/tools/umi_tools/umi-tools_dedup.xml b/tools/umi_tools/umi-tools_dedup.xml
@@ -5,7 +5,7 @@
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements">
-        <requirement type="package" version="1.12">samtools</requirement>
+        <requirement type="package" version="1.21">samtools</requirement>
     </expand>
     <command detect_errors="exit_code"><![CDATA[
         @LINK_SAM_BAM_INPUT@

diff --git a/tools/umi_tools/umi-tools_group.xml b/tools/umi_tools/umi-tools_group.xml
@@ -5,7 +5,7 @@
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements">
-        <requirement type="package" version="1.12">samtools</requirement>
+        <requirement type="package" version="1.21">samtools</requirement>
     </expand>
     <command detect_errors="exit_code"><![CDATA[
         @LINK_SAM_BAM_INPUT@