Mercurial > repos > lparsons > htseq_count

diff htseq-count.xml @ 3:f7a5b54a8d4f

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Split feature and non-feature counts, removed tool_dependencies.xml (for now)
author Lance Parsons <lparsons@princeton.edu>
date Mon, 10 Sep 2012 17:30:10 -0400
parents 3fdeebd7e710
children 14bec14f4290
line wrap: on
line diff
--- a/htseq-count.xml	Tue Sep 04 14:16:33 2012 -0400
+++ b/htseq-count.xml	Mon Sep 10 17:30:10 2012 -0400
@@ -1,4 +1,4 @@
-<tool id="htseq_count" name="htseq-count" version="0.1">
+<tool id="htseq_count" name="htseq-count" version="0.2">
     <description> - Count aligned reads in a BAM file that overlap features in a GFF file</description>
     <version_command>htseq-count -h | grep version | sed 's/^\(.*\)*\(version .*\)\./\2/'</version_command>
     <requirements>
@@ -35,7 +35,7 @@
         $samfile 
     #end if
     $gfffile 
-    &gt; $counts
+    | awk '{if ($1 ~ "no_feature|ambiguous|too_low_aQual|not_aligned|alignment_not_unique") print $0 | "cat 1>&amp;2"; else print $0}' &gt; $counts 2&gt;$othercounts
     #if $samout_conditional.samout:
         &amp;&amp; samtools view -Su -t ${reference_fasta_filename}.fai $__new_file_path__/${samoutfile.id}_tmp | samtools sort -o - sorted > $samoutfile
     #end if</command>
@@ -93,6 +93,7 @@
 
     <outputs>
         <data format="tabular" name="counts" label="${tool.name} on ${on_string}"/>
+        <data format="tabular" name="othercounts" label="${tool.name} on ${on_string} (no feature)"/>
         <data format="bam" name="samoutfile" label="${tool.name} on ${on_string} (BAM)">
             <filter>samout_conditional['samout']</filter>
         </data>
@@ -108,12 +109,14 @@
             <param name="gfffile" value="htseq-test.gff" />
             <param name="samout" value="False" />
             <output name="counts" file="htseq-test_counts.tsv" />
+            <output name="othercounts" file="htseq-test_othercounts.tsv" />
         </test>
         <test>
             <param name="samfile" value="htseq-test.bam" />
             <param name="gfffile" value="htseq-test.gff" />
             <param name="samout" value="False" />
             <output name="counts" file="htseq-test_counts.tsv" />
+            <output name="othercounts" file="htseq-test_othercounts.tsv" />
         </test>
         <!-- Seems to be an issue setting the $reference_fasta_filename variable during test
         <test>
@@ -123,6 +126,7 @@
             <param name="reference_source_selector" value="history" />
             <param name="ref_file" value="htseq-test_reference.fasta" />
             <output name="counts" file="htseq-test_counts.tsv" />
+            <output name="othercounts" file="htseq-test_othercounts.tsv" />
             <output name="samoutfile" file="htseq-test_samout.bam" />
         </test>
         -->