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galaxyproteomics · Sep 4, 2023 · c67ed43 · c67ed43
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Showing 4 changed files with 39 additions and 48 deletions.
diff --git a/tools/eggnog_mapper/eggnog_macros.xml b/tools/eggnog_mapper/eggnog_macros.xml
@@ -426,6 +426,22 @@ python '${__tool_directory__}/data_manager_eggnog.py' --config_file '$out_file'
         #end if
     ]]></token>
 
+    <!-- output options applying to search step -->
+    <xml name="output_options_macro">
+        <section name="output_options" expanded="false" title="Output Options">
+            <param argument="--no_file_comments" type="boolean" truevalue="--no_file_comments" falsevalue="" checked="true"
+                label="Exclude header lines and stats from output files"/>
+            <yield/>
+        </section>
+    </xml>
+    <!-- output options applying search and annotate step -->
+    <xml name="output_options_annotate_macro">
+        <expand macro="output_options_macro">
+            <param argument="--report_orthologs" type="boolean" truevalue="--report_orthologs" falsevalue="" checked="false" label="Output a file with the list of orthologs for each hit"/>
+            <param argument="--md5" type="boolean" truevalue="--md5" falsevalue="" checked="false" label="Add md5 hash of each query to annotations"/>
+        </expand>
+    </xml>
+
     <token name="@SEED_ORTHOLOG_COLUMNS@">query_name,seed_eggNOG_ortholog,seed_ortholog_evalue,seed_ortholog_score,query_start,query_end,seed_start,seed_end,pident,query_cov,seed_cov</token>
 
     <xml name="ortho_search_outputs_macro">
@@ -437,14 +453,25 @@ python '${__tool_directory__}/data_manager_eggnog.py' --config_file '$out_file'
         </data>
     </xml>
 
-    <xml name="seed_orthologs_assertion">
+    <xml name="seed_orthologs_assertion" token_nocomments="true">
         <output name="seed_orthologs" ftype="tabular">
             <assert_contents>
                 <has_line line="#qseqid&#009;sseqid&#009;evalue&#009;bitscore&#009;qstart&#009;qend&#009;sstart&#009;send&#009;pident&#009;qcov&#009;scov"/>
                 <has_line_matching expression="(\S+\t){2}[-+.e\d]+\t[.\d]+(\t\d+){4}(\t[.\d]+){3}" n="1"/>
+                <has_line_matching expression="##.*" negate="@NOCOMMENTS@"/>
             </assert_contents>
         </output>
     </xml>
+
+    <token name="@HELP_SEARCH_OUTPUTS@"><![CDATA[
+        **seed orthologs**
+        
+        each line in the file provides the best match of each query within the best Orthologous Group (OG)
+        reported in the [project].hmm_hits file, obtained running PHMMER against all sequences within the best OG.
+        The seed ortholog is used to fetch fine-grained orthology relationships from eggNOG.
+        If using the diamond search mode, seed orthologs are directly
+        obtained from the best matching sequences by running DIAMOND against the whole eggNOG protein space.
+    ]]></token>
 
     <!-- macros and tokens for annotate -->
 
@@ -522,35 +549,28 @@ python '${__tool_directory__}/data_manager_eggnog.py' --config_file '$out_file'
         </data>
     </xml>
 
-    <xml name="annotations_assertion" token_columns="21" token_add_metadata_columm_names="" token_add_column_names="" token_add_column_re="">
+    <xml name="annotations_assertion" token_columns="21" token_add_metadata_columm_names="" token_add_column_names="" token_add_column_re="" token_nocomments="true">
         <output name="annotations" ftype="tabular">
             <metadata name="columns" value="@COLUMNS@" />
             <!-- <metadata name="column_names" value="query,seed_ortholog,evalue,score,max_annot_lvl,COG_category,Description,Preferred_name,GOs,EC,KEGG_ko,KEGG_Pathway,KEGG_Module,KEGG_Reaction,KEGG_rclass,BRITE,KEGG_TC,CAZy,BiGG_Reaction,PFAMseggNOG_OGs@ADD_METADATA_COLUMN_NAMES@" /> -->
             <assert_contents>
                 <has_line line="#query&#009;seed_ortholog&#009;evalue&#009;score&#009;eggNOG_OGs&#009;max_annot_lvl&#009;COG_category&#009;Description&#009;Preferred_name&#009;GOs&#009;EC&#009;KEGG_ko&#009;KEGG_Pathway&#009;KEGG_Module&#009;KEGG_Reaction&#009;KEGG_rclass&#009;BRITE&#009;KEGG_TC&#009;CAZy&#009;BiGG_Reaction&#009;PFAMs@ADD_COLUMN_NAMES@"/>
                 <has_line_matching expression="(\S+\t){2}[-+.e\d]+\t[.\d]+(\t\S+){7}\tko:\S+(\t\S+){9}@ADD_COLUMN_RE@" n="1"/>
+                <has_line_matching expression="##.*" negate="@NOCOMMENTS@"/>
             </assert_contents>
         </output>
     </xml>
-    <xml name="annotations_orthologs_assertion">
+    <xml name="annotations_orthologs_assertion" token_nocomments="true">
         <output name="annotations_orthologs" ftype="tabular">
             <metadata name="columns" value="4" />
             <metadata name="column_names" value="query,orth_type,species,orthologs" />
             <assert_contents>
                 <has_line line="#query&#009;orth_type&#009;species&#009;orthologs"/>
                 <has_line_matching expression="\S+\t(one2one|many2one|one2many|many2many|seed)(\t[^\t]+){2}" n="2"/>
+                <has_line_matching expression="##.*" negate="@NOCOMMENTS@"/>
             </assert_contents>
         </output>
     </xml>
-    <token name="@HELP_SEARCH_OUTPUTS@"><![CDATA[
-        **seed orthologs**
-        
-        each line in the file provides the best match of each query within the best Orthologous Group (OG)
-        reported in the [project].hmm_hits file, obtained running PHMMER against all sequences within the best OG.
-        The seed ortholog is used to fetch fine-grained orthology relationships from eggNOG.
-        If using the diamond search mode, seed orthologs are directly
-        obtained from the best matching sequences by running DIAMOND against the whole eggNOG protein space.
-    ]]></token>
     <token name="@HELP_ANNOTATION_OUTPUTS@"><![CDATA[
         **annotations**
 

diff --git a/tools/eggnog_mapper/eggnog_mapper/eggnog_mapper.xml b/tools/eggnog_mapper/eggnog_mapper/eggnog_mapper.xml
@@ -38,14 +38,7 @@
             <when value="--no_annot"/>
         </conditional>
 
-        <section name="output_options" expanded="false" title="Output Options">
-            <param argument="--no_file_comments" type="boolean" truevalue="--no_file_comments" falsevalue="" checked="true"
-                label="Exclude header lines and stats from output files"/>
-            <param argument="--report_orthologs" type="boolean" truevalue="--report_orthologs" falsevalue="" checked="false"
-                label="Output a file with the list of orthologs for each hit"/>
-            <param argument="--md5" type="boolean" truevalue="--md5" falsevalue="" checked="false"
-                label="Add md5 hash of each query to annotations"/>
-        </section>
+        <expand macro="output_options_annotate_macro"/>
     </inputs>
     <outputs>
         <expand macro="ortho_search_outputs_macro"/>
@@ -65,7 +58,6 @@
                 <param name="no_annot" value="--no_annot"/>
             </conditional>
             <section name="output_options">
-                <param name="no_file_comments" value="true"/>
             </section>
             <expand macro="seed_orthologs_assertion"/>
             <expand macro="stdout_assertion"/>
@@ -84,7 +76,6 @@
             </conditional>
             <section name="output_options">
                 <param name="report_orthologs" value="true"/>
-                <param name="no_file_comments" value="true"/>
             </section>
             <expand macro="annotations_assertion"/>
             <expand macro="annotations_orthologs_assertion"/>
@@ -99,12 +90,12 @@
             </conditional>
             <section name="output_options">
                 <param name="report_orthologs" value="true"/>
-                <param name="no_file_comments" value="true"/>
+                <param name="no_file_comments" value="false"/>
                 <param name="md5" value="true"/>
             </section>
-            <expand macro="seed_orthologs_assertion"/>
-            <expand macro="annotations_assertion" columns="22" add_metadata_columm_names=",md5" add_column_names="&#009;md5" add_column_re="\t[\d\w]+"/>
-            <expand macro="annotations_orthologs_assertion"/>
+            <expand macro="seed_orthologs_assertion" nocomments="false"/>
+            <expand macro="annotations_assertion" columns="22" add_metadata_columm_names=",md5" add_column_names="&#009;md5" add_column_re="\t[\d\w]+" nocomments="false"/>
+            <expand macro="annotations_orthologs_assertion" nocomments="false"/>
             <expand macro="stdout_assertion"/>
         </test>
 
@@ -118,7 +109,6 @@
             </conditional>
             <section name="output_options">
                 <param name="report_orthologs" value="true"/>
-                <param name="no_file_comments" value="true"/>
                 <param name="md5" value="true"/>
             </section>
             <expand macro="annotations_assertion" columns="22" add_metadata_columm_names=",md5" add_column_names="&#009;md5" add_column_re="\t[\d\w]+"/>
@@ -141,7 +131,6 @@
             </section>
             <section name="output_options">
                 <param name="report_orthologs" value="true"/>
-                <param name="no_file_comments" value="true"/>
             </section>
             <expand macro="seed_orthologs_assertion"/>
             <expand macro="annotations_assertion"/>
@@ -161,7 +150,6 @@
             </conditional>
             <section name="output_options">
                 <param name="report_orthologs" value="true"/>
-                <param name="no_file_comments" value="true"/>
             </section>
             <expand macro="seed_orthologs_assertion"/>
             <expand macro="annotations_assertion"/>

diff --git a/tools/eggnog_mapper/eggnog_mapper/eggnog_mapper_annotate.xml b/tools/eggnog_mapper/eggnog_mapper/eggnog_mapper_annotate.xml
@@ -37,14 +37,7 @@
             <expand macro="annotation_options_macro"/>
         </section>
 
-        <section name="output_options" expanded="false" title="Output Options">
-            <param argument="--no_file_comments" type="boolean" truevalue="--no_file_comments" falsevalue="" checked="true"
-                label="Exclude header lines and stats from output files"/>
-            <param argument="--report_orthologs" type="boolean" truevalue="--report_orthologs" falsevalue="" checked="false"
-                label="Output a file with the list of orthologs for each hit"/>
-            <param argument="--md5" type="boolean" truevalue="--md5" falsevalue="" checked="false"
-                label="Add md5 hash of each query to annotations"/>
-        </section>
+        <expand macro="output_options_annotate_macro"/>
     </inputs>
     <outputs>
         <expand macro="annotation_output_macro"/>

diff --git a/tools/eggnog_mapper/eggnog_mapper/eggnog_mapper_search.xml b/tools/eggnog_mapper/eggnog_mapper/eggnog_mapper_search.xml
@@ -11,8 +11,6 @@
         @ORTHO_SEARCH_TOKEN@
 
         $output_options.no_file_comments
-        $output_options.report_orthologs
-        $output_options.md5
         --output='results'
         --cpu "\${GALAXY_SLOTS:-4}"
         --scratch_dir \${TEMP:-\$_GALAXY_JOB_TMP_DIR}
@@ -21,14 +19,7 @@
     <inputs>
         <expand macro="db_macro"/>
         <expand macro="ortho_search_macro"/>
-        <section name="output_options" expanded="false" title="Output Options">
-            <param argument="--no_file_comments" type="boolean" truevalue="--no_file_comments" falsevalue="" checked="true"
-                label="Exclude header lines and stats from output files"/>
-            <param argument="--report_orthologs" type="boolean" truevalue="--report_orthologs" falsevalue="" checked="false"
-                label="Output a file with the list of orthologs for each hits"/>
-            <param argument="--md5" type="boolean" truevalue="--md5" falsevalue="" checked="false"
-                label="Add md5 hash of each query to annotations"/>
-        </section>
+        <expand macro="output_options_macro"/>
     </inputs>
     <outputs>
         <expand macro="ortho_search_outputs_macro"/>
@@ -56,7 +47,6 @@
                 <param name="sensmode" value="fast" />
             </conditional>
             <section name="output_options">
-                <param name="report_orthologs" value="true"/>
                 <param name="no_file_comments" value="true"/>
             </section>
             <expand macro="seed_orthologs_assertion"/>