diff gffcompare.xml @ 2:f99d7825a501 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit a5352fb7f073b0083b750c5cf7d283ebcc16b30d

--- a/gffcompare.xml	Wed Dec 12 03:19:14 2018 -0500
+++ b/gffcompare.xml	Tue Feb 05 15:51:44 2019 -0500
@@ -1,16 +1,10 @@
-<tool id="gffcompare" name="GffCompare" version="0.9.8+galaxy1">
+<tool id="gffcompare" name="GffCompare" version="0.10.6">
     <description>compare assembled transcripts to a reference annotation</description>
     <requirements>
-        <requirement type="package" version="0.9.8">gffcompare</requirement>
+        <requirement type="package" version="0.10.6">gffcompare</requirement>
     </requirements>
-    <stdio>
-        <exit_code range="1:" />
-        <exit_code range=":-1" />
-        <regex match="Error" />
-        <regex match="Exception" />
-    </stdio>
     <version_command>gffcompare -v | awk '{print $2}'</version_command>
-    <command><![CDATA[
+    <command detect_errors="aggressive"><![CDATA[
 #import re
 #set escaped_element_identifiers = [re.sub('[^\w\-]', '_', str(_.element_identifier)) for _ in $gffinputs]
 #for $input, $escaped_element_identifier in zip($gffinputs, $escaped_element_identifiers):
@@ -43,11 +37,16 @@
 $discard_single_exon
 -e $max_dist_exon
 -d $max_dist_group
-$discard_intron_redundant_transfrags
+-p '$adv_output.p'
+$adv_output.A
+$adv_output.C
+$adv_output.X
+$adv_output.K
 
 #for $escaped_element_identifier in $escaped_element_identifiers:
     '$escaped_element_identifier'
 #end for
+
     ]]></command>
     <inputs>
         <param format="gtf" name="gffinputs" type="data" label="GTF inputs for comparison" help="" multiple="true" />
@@ -101,7 +100,13 @@
         </param>
         <param argument="-e" help="max. distance (range) allowed from free ends of terminal exons of reference transcripts when assessing exon accuracy. Default: 100" label="Max. Distance for assessing exon accuracy" name="max_dist_exon" type="integer" value="100" />
         <param argument="-d" help="max. distance (range) for grouping transcript start sites. Default: 100" label="Max distance for transcript grouping" name="max_dist_group" type="integer" value="100" />
-        <param argument="-F" help="Discard intron-redundant transfrags if they share the 5' end (if they differ only at the 3' end)" truevalue="-F" falsevalue="" label="discard intron-redundant transfrags sharing 5'" name="discard_intron_redundant_transfrags" type="boolean" />
+        <section name="adv_output" title="Options for the annotated/combined GTF output file">
+            <param argument="-p"  type="text" value="TCONS" label="name prefix for consensus transcripts" help="for combined.gtf (default: 'TCONS')" />
+            <param argument="-C"  type="boolean" checked="false" truevalue="-C" falsevalue=""  label="discard the 'contained' transfrags" help="i.e. collapse intron-redundant transfrags across all query files" />
+            <param argument="-A"  type="boolean" checked="false" truevalue="-A" falsevalue=""  label="discard the 'contained' transfrags except intron-redundant transfrags starting with a different 5' exon" help="like -C but does not discard intron-redundant transfrags if they start with a different 5' exon" />
+            <param argument="-X"  type="boolean" checked="false" truevalue="-X" falsevalue=""  label="discard the 'contained' transfrags also if ends stick out within the container's introns" help="like -C but also discard contained transfrags if transfrag ends stick out within the container's introns" />
+            <param argument="-K"  type="boolean" checked="false" truevalue="-A" falsevalue=""  label="do NOT discard any redundant transfrag matching a reference" help="for -C/-A/-X" />
+        </section>
     </inputs>
     <outputs>
         <data format="txt" from_work_dir="gffcmp.stats" label="${tool.name} on ${on_string}: transcript accuracy" name="transcripts_stats" />
@@ -135,7 +140,6 @@
             <param name="discard_single_exon" value="" />
             <param name="max_dist_exon" value="100" />
             <param name="max_dist_group" value="100" />
-            <param name="discard_intron_redundant_transfrags" value="No" />
             <output file="gffcompare_out1.stats" name="transcripts_stats" lines_diff="6" />
             <output file="gffcompare_out1.loci" name="transcripts_loci" lines_diff="2" />
             <output file="gffcompare_out1.tracking" name="transcripts_tracking" />
@@ -162,7 +166,6 @@
             <param name="discard_single_exon" value="" />
             <param name="max_dist_exon" value="100" />
             <param name="max_dist_group" value="100" />
-            <param name="discard_intron_redundant_transfrags" value="No" />
             <output file="gffcompare_out2.stats" name="transcripts_stats" lines_diff="6" />
             <output file="gffcompare_out2.loci" name="transcripts_loci" />
             <output file="gffcompare_out2.tracking" name="transcripts_tracking" />
@@ -183,7 +186,7 @@
 (see manual: http://cole-trapnell-lab.github.io/cufflinks/cuffcompare/). Most of the options and parameters of CuffCompare
 are supported by GffCompare, while new features will likely be added to GffCompare in the future.
 
-A notable difference from GffCompare is that when a single query GTF/GFF file is given as input, along with a reference annotation (-r option),
+A notable difference of GffCompare is that when a single query GTF/GFF file is given as input, along with a reference annotation (-r option),
 gffcompare switches into "annotation mode" and it generates a .annotated.gtf file instead of the .merged.gtf produced by CuffCompare with the
 same parameters. This file has the same general format as CuffCompare's .merged.gtf file (with "class codes" assigned to transcripts as per
 their relationship with the matching/overlapping reference transcript),  but the original transcript IDs are preserved, so gffcompare can thus