# HG changeset patch
# User jjohnson
# Date 1574712564 18000
# Node ID 9a01840eac52896900df924e28efb6328820b9e9
# Parent  86cd2e70b0dc95e0b9afa1ed4479e9eee2829438
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 6b978e61a7f66160f2577d907f52dd641f103986-dirty

diff -r 86cd2e70b0dc -r 9a01840eac52 cat_bins.xml
--- a/cat_bins.xml	Sun Nov 24 22:35:05 2019 -0500
+++ b/cat_bins.xml	Mon Nov 25 15:09:24 2019 -0500
@@ -24,6 +24,10 @@
     @USE_INTERMEDIATES@
     @CUSTOM_SETTINGS@
     && @TXT2TSV@ *.ORF2LCA.txt *.bin2classification.txt
+    #if len($mags) > 1:
+        #set pat = '$' + '{i/concatenated./}'
+        && (for i in *.concatenated.*; do ln -s "\$i" "${pat}"; done)
+    #end if
     @ADD_NAMES@
     @SUMMARISE@
     ]]></command>
diff -r 86cd2e70b0dc -r 9a01840eac52 macros.xml
--- a/macros.xml	Sun Nov 24 22:35:05 2019 -0500
+++ b/macros.xml	Mon Nov 25 15:09:24 2019 -0500
@@ -120,12 +120,12 @@
         && CAT add_names $names.only_official $names.exclude_scores 
             @CAT_TAXONOMY@
             #if $bcat == 'CAT'
-                -i cat_output.contigs2classification.tsv
+                -i cat_output.contig2classification.tsv
             #else
                 -i cat_output.bin2classification.tsv
             #end if
             -o classification_names.txt
-        && @TXT2TSV@ -i classification_names -o $classification_names
+        && @TXT2TSV@ -i classification_names.txt -o $classification_names
     #end if
     #if $names.add_names in ['orf2lca','both']:
         && CAT add_names $names.only_official $names.exclude_scores 
@@ -146,11 +146,11 @@
         #if $names.add_names in ['classification','both'] and $names.only_official: 
             #set $summary_input = $classification_names
         #else 
-            #set $summary_input = classification_offical_names
+            #set $summary_input = 'classification_offical_names'
             && CAT add_names --only_official
                 @CAT_TAXONOMY@
                 #if $bcat == 'CAT'
-                    -i cat_output.contigs2classification.tsv
+                    -i cat_output.contig2classification.tsv
                 #else
                     -i cat_output.bin2classification.tsv
                 #end if
@@ -168,7 +168,7 @@
     
     <xml name="select_outputs">
         <param name="select_outputs" type="select" multiple="true" optional="false" label="Select outputs">
-            <option value="log" selected="true">CAT.log</option>
+            <option value="log" selected="true">log</option>
             <option value="predicted_proteins_faa" selected="true">predicted_proteins.faa</option>
             <option value="predicted_proteins_gff">predicted_proteins.gff</option>
             <option value="alignment_diamond">alignment.diamond</option>
@@ -179,6 +179,8 @@
     <xml name="select_cat_outputs">
         <param name="bcat" type="hidden" value="CAT"/>
         <param name="seqtype" type="hidden" value="contig"/>
+        <param name="sum_titles" type="hidden" value="contigs,number of ORFs,number of positions"/>
+        <param name="bin_col" type="hidden" value=""/>
         <expand macro="select_outputs">
             <option value="contig2classification" selected="true">contig2classification.txt</option>
         </expand>
@@ -186,6 +188,8 @@
     <xml name="select_bat_outputs">
         <param name="bcat" type="hidden" value="BAT"/>
         <param name="seqtype" type="hidden" value="bin"/>
+        <param name="sum_titles" type="hidden" value="bins"/>
+        <param name="bin_col" type="hidden" value="bin,"/>
         <expand macro="select_outputs">
             <option value="bin2classification" selected="true">bin2classification.txt</option>
         </expand>
@@ -215,7 +219,7 @@
             <filter>'orf2lca' in select_outputs</filter>
             <actions>
                 <action name="comment_lines" type="metadata" default="1" />
-                <action name="column_names" type="metadata" default="ORF,lineage,bit-score" />
+                <action name="column_names" type="metadata" default="ORF,${bin_col}lineage,bit-score" />
             </actions>
         </data>
         <data name="contig2classification" format="tabular" label="${bcat}.contig2classification.txt" from_work_dir="cat_output.contig2classification.tsv">
@@ -233,14 +237,14 @@
             </actions>
         </data>
         <data name="orf2lca_names" format="tabular" label="${bcat}.ORF2LCA.names.txt">
-            <filter>'orf2lca' in names.add_names</filter>
+            <filter>names['add_names'] in ['both','orf2lca']</filter>
             <actions>
                 <action name="comment_lines" type="metadata" default="1" />
-                <action name="column_names" type="metadata" default="ORF,lineage,bit-score,superkingdom,phylum,class,order,family,genus,species" />
+                <action name="column_names" type="metadata" default="ORF,${bin_col}lineage,bit-score,superkingdom,phylum,class,order,family,genus,species" />
             </actions>
         </data>
         <data name="classification_names" format="tabular" label="${bcat}.${seqtype}2classification.names.txt">
-            <filter>'classification' in names.add_names</filter>
+            <filter>names['add_names'] in ['both','classification']</filter>
             <actions>
                 <action name="comment_lines" type="metadata" default="1" />
                 <action name="column_names" type="metadata" default="${seqtype},classification,reason,lineage,lineage scores,superkingdom,phylum,class,order,family,genus,species" />
@@ -249,8 +253,8 @@
         <data name="classification_summary" format="tabular" label="${bcat}.${seqtype}2classification.summary.txt">
             <filter>'classification' in summarise</filter>
             <actions>
-                <action name="comment_lines" type="metadata" default="1" />
-                <action name="column_names" type="metadata" default="rank,clade,number of contigs,number of ORFs,number of positions" />
+                <action name="comment_lines" type="metadata" default="4" />
+                <action name="column_names" type="metadata" default="rank,clade,number of ${sum_titles}" />
             </actions>
         </data>
     </xml>
diff -r 86cd2e70b0dc -r 9a01840eac52 tabpad.py
--- a/tabpad.py	Sun Nov 24 22:35:05 2019 -0500
+++ b/tabpad.py	Mon Nov 25 15:09:24 2019 -0500
@@ -7,13 +7,24 @@
 def padfile(infile, outfile, fieldcnt=None):
     with open(infile, 'r') as fh:
         out = open(outfile, 'w')
+        commentlines = []
         tabs = '\t' * fieldcnt if fieldcnt is not None else None
-        for i, txtline in enumerate(fh):
+        def pad_line(txtline, tabs=None):
             line = txtline.rstrip('\r\n')
             fields = line.split('\t')
             if not tabs:
                 tabs = '\t' * len(fields)
             out.write('%s%s\n' % (line, tabs[len(fields):]))
+        for i, txtline in enumerate(fh):
+            if txtline.lstrip().startswith('#'):
+                commentlines.append(txtline)
+            else:
+                if commentlines:
+                    for i in range(len(commentlines)-1):
+                        out.write(commentlines[i])
+                    pad_line(commentlines[-1], tabs=tabs)
+                    commentlines = []
+                pad_line(txtline, tabs=tabs)
         out.close()