diff stringtie_merge.xml @ 11:6e45b443ef1f draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf

--- a/stringtie_merge.xml	Tue Apr 04 12:58:27 2017 -0400
+++ b/stringtie_merge.xml	Thu Jun 01 12:16:04 2017 -0400
@@ -1,17 +1,16 @@
-<tool id="stringtie_merge" name="StringTie" version="1.3.3">
-    <description>merge transcripts</description>
+<tool id="stringtie_merge" name="StringTie merge" version="1.3.3">
+    <description>transcripts</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
     <expand macro="stdio" />
     <expand macro="version_command" />
-    <command>
-    <![CDATA[
+    <command><![CDATA[
         stringtie --merge
         -p \${GALAXY_SLOTS:-1}
         #if $guide_gff:
-            -G "$guide_gff"
+            -G '$guide_gff'
         #end if
         -m $min_len
         -c $min_cov
@@ -20,38 +19,37 @@
         -f $min_iso
         -g $gap_len
         $keep_introns
-        #set inputs = '" "'.join(str($input_gtf).split(','))
-        -o $out_gtf "$inputs"
-    ]]>
-    </command>
+        #set inputs = "' '".join(str($input_gtf).split(','))
+        -o '$out_gtf' '$inputs'
+    ]]></command>
     <inputs>
-        <param type="data" name="input_gtf" multiple="True" format="gtf,gff3" />
-        <param type="data" name="guide_gff" optional="True" format="gtf,gff3" />
-        <param argument="-m" type="integer" name="min_len" value="50" help="Minimum input transcript length to include in the merge" />
-        <param argument="-c" type="integer" name="min_cov" value="0" help="Minimum input transcript coverage to include in the merge" />
-        <param argument="-F" type="float" name="min_fpkm" value="1.0" help="Minimum input transcript FPKM to include in the merge" />
-        <param argument="-T" type="float" name="min_tpm" value="1.0" help="Minimum input transcript TPM to include in the merge" />
-        <param argument="-f" type="float" name="min_iso" value="0.01" help="Minimum isoform fraction" />
-        <param argument="-g" type="integer" name="gap_len" value="250" help="Gap between transcripts to merge together" />
-        <param argument="-i" type="boolean" truevalue="-i" falsevalue="" name="keep_introns" help="Keep merged transcripts with retained introns" />
+        <param name="input_gtf" type="data" format="gtf,gff3" multiple="true" label="Transcripts" help="In GTF or GFF3 format" />
+        <param name="guide_gff" argument="-G" type="data" format="gtf,gff3" optional="true" label="Reference annotation to include in the merging" />
+        <param name="min_len" argument="-m" type="integer" value="50" label="Minimum input transcript length to include in the merge" />
+        <param name="min_cov" argument="-c" type="integer" value="0" label="Minimum input transcript coverage to include in the merge" />
+        <param name="min_fpkm" argument="-F" type="float" value="1.0" label="Minimum input transcript FPKM to include in the merge" />
+        <param name="min_tpm" argument="-T" type="float" value="1.0" label="Minimum input transcript TPM to include in the merge" />
+        <param name="min_iso" argument="-f" type="float" value="0.01" label="Minimum isoform fraction" />
+        <param name="gap_len" argument="-g" type="integer" value="250" label="Gap between transcripts to merge together" />
+        <param name="keep_introns" argument="-i" type="boolean" truevalue="-i" falsevalue="" label="Keep merged transcripts with retained introns" help="By default these are not kept unless there is strong evidence for them" />
     </inputs>
     <outputs>
         <data name="out_gtf" format="gtf" />
     </outputs>
     <tests>
         <test>
-            <param ftype="gtf" name="input_gtf" value="stringtie_out1.gtf,stringtie_out2.gtf,stringtie_out3.gtf,stringtie_out4.gtf" />
-            <param ftype="gtf" name="guide_gff" value="stringtie_in.gtf" />
-            <output file="stringtie_merge_out1.gtf" ftype="gtf" lines_diff="2" name="out_gtf" />
+            <param name="input_gtf" ftype="gtf" value="stringtie_out1.gtf,stringtie_out2.gtf,stringtie_out3.gtf,stringtie_out4.gtf" />
+            <param name="guide_gff" ftype="gtf" value="stringtie_in.gtf" />
+            <output name="out_gtf" file="stringtie_merge_out1.gtf" ftype="gtf" lines_diff="2" />
         </test>
         <test>
-            <param ftype="gtf" name="input_gtf" value="stringtie_merge_in1.gtf,stringtie_merge_in2.gtf" />
-            <param ftype="gtf" name="guide_gff" value="stringtie_merge_in3.gtf" />
-            <output file="stringtie_merge_out2.gtf" ftype="gtf" lines_diff="2" name="out_gtf" />
+            <param name="input_gtf" ftype="gtf" value="stringtie_merge_in1.gtf,stringtie_merge_in2.gtf" />
+            <param name="guide_gff" ftype="gtf" value="stringtie_merge_in3.gtf" />
+            <output name="out_gtf" file="stringtie_merge_out2.gtf" ftype="gtf" lines_diff="2" />
         </test>
         <test>
-            <param ftype="gtf" name="input_gtf" value="stringtie_merge_in1.gtf,stringtie_merge_in2.gtf" />
-            <output ftype="gtf" name="out_gtf">
+            <param name="input_gtf" ftype="gtf" value="stringtie_merge_in1.gtf,stringtie_merge_in2.gtf" />
+            <output name="out_gtf" ftype="gtf">
                 <assert_contents>
                     <has_text text="stringtie --merge" />
                 </assert_contents>
@@ -59,35 +57,13 @@
         </test>
     </tests>
     <help><![CDATA[
-
 **What it does?**
 
-This is a special usage mode of StringTie_, distinct from the assembly usage mode. In the merge mode, StringTie takes as input a list of GTF/GFF files and merges/assembles these transcripts into a non-redundant set of transcripts. This mode is used in the new differential analysis pipeline to generate a global, unified set of transcripts (isoforms) across multiple RNA-Seq samples. 
+This is a special usage mode of StringTie_, distinct from the assembly usage mode. In the merge mode, StringTie takes as input a list of GTF/GFF files and merges/assembles these transcripts into a non-redundant set of transcripts. This mode is used in the new differential analysis pipeline to generate a global, unified set of transcripts (isoforms) across multiple RNA-Seq samples.
 
-If a reference annotation is provided, StringTie will assemble the transfrags from the input GTF files with the reference transcripts. 
+If a reference annotation is provided, StringTie will assemble the transfrags from the input GTF files with the reference transcripts.
 
 .. _StringTie: http://ccb.jhu.edu/software/stringtie/
-
-------
-
-StringTie --merge has the following options::
-
-  -G <guide_gff>   reference annotation to include in the merging (GTF/GFF3)
-  -o <out_gtf>     output file name for the merged transcripts GTF
-                    (default: stdout)
-  -m <min_len>     minimum input transcript length to include in the merge
-                    (default: 50)
-  -c <min_cov>     minimum input transcript coverage to include in the merge
-                    (default: 0)
-  -F <min_fpkm>    minimum input transcript FPKM to include in the merge
-                    (default: 1.0)
-  -T <min_tpm>     minimum input transcript TPM to include in the merge
-                    (default: 1.0)
-  -f <min_iso>     minimum isoform fraction (default: 0.01)
-  -g <gap_len>     gap between transcripts to merge together (default: 250)
-  -i               keep merged transcripts with retained introns; by default
-                   these are not kept unless there is strong evidence for them
-  -l <label>       name prefix for output transcripts (default: MSTRG)
     ]]></help>
     <expand macro="citations" />
 </tool>