diff probamconvert.xml @ 1:37369e255465 draft default tip

Uploaded

--- a/probamconvert.xml	Tue Mar 14 17:06:41 2017 -0400
+++ b/probamconvert.xml	Wed Mar 15 09:43:14 2017 -0400
@@ -7,9 +7,9 @@
         <exit_code range="1:" />
     </stdio>
     <command><![CDATA[
-        #set $psm_file = input.${input.datatype.file_ext}
+        #set $psm_file = 'input.'+str($input.datatype.file_ext)
         ln -s "$input" $psm_file;
-        proBAM.py --name="converted" --file=$psm_file 
+        proBAM.py --name="converted" --file=$psm_file --conversion_mode=$conversion_mode
         --database=$refsrc.database
         #if str($refsrc.database) == 'ENSEMBL':
             --species=$refsrc.species
@@ -17,15 +17,14 @@
                 --version=$refsrc.version
             #end if
         #end if
-        #if str($optional.decoy_annotation) != 'None':
+        #if str($optional.decoy_annotation) != '':
             --decoy_annotation='$optional.decoy_annotation'
         #end if
-        --pre_picked_annotation=$pre_picked_annotation
+        --pre_picked_annotation=$optional.pre_picked_annotation
         --mismatches=$optional.mismatches
         $optional.rm_duplicates
         $optional.three_frame_translation
         $optional.include_unmapped
-        --directory=outputs
     ]]></command>
     <inputs>
         <param name="input" type="data" format="mzid,pepxml" label="Peptide Indentification (mzIdentML or pepXML)"/>
@@ -87,21 +86,21 @@
          </section>
     </inputs>
     <outputs>
-        <data name="output_bam" format="pro.bam" label="" from_work_dir="outputs/converted.sorted.bam">
+        <data name="output_bam" format="bam" label="${conversion_mode} ${input.display_name}.pro.bam" from_work_dir="converted.sorted.bam">
             <filter>conversion_mode != 'proBED'</filter>
         </data>
-        <data name="output_bed" format="pro.bed" label="" from_work_dir="outputs/converted.pro.bed">
+        <data name="output_bed" format="bed" label="${conversion_mode} ${input.display_name}.pro.bed" from_work_dir="converted.pro.bed">
             <filter>conversion_mode == 'proBED'</filter>
         </data>
     </outputs>
     <tests>
         <test>
             <param name="input" ftype="mzid" value="test.mzid"/>
-            <param name="conversion_mode" value="proBAM_psm"/>
+            <param name="conversion_mode" value="proBED"/>
             <param name="database" value="ENSEMBL"/>
             <param name="species" value="homo_sapiens"/>
             <param name="version" value="87"/>
-            <output name="output_bam">
+            <output name="output_bed">
                 <assert_contents>
                     <has_text text="Q7Z6Z7_0" />
                 </assert_contents>