Mercurial > repos > fubar > htseq_bams_to_count_matrix

changeset 49:c57e63d1a9d2 draft

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working test. first upload
author fubar
date Fri, 02 Jan 2015 03:32:39 -0500
parents 58fe9656873a
children 0edc994d4021
files htseqsams2mx.xml test-data/generatetest.sh tool_dependencies.xml
diffstat 3 files changed, 12 insertions(+), 25 deletions(-) [+]
line wrap: on
line diff
--- a/htseqsams2mx.xml	Thu Nov 21 18:05:49 2013 -0500
+++ b/htseqsams2mx.xml	Fri Jan 02 03:32:39 2015 -0500
@@ -10,13 +10,10 @@
   </requirements>
   <command interpreter="python">
     htseqsams2mx.py -g "$gfffile" -o "$outfile" -m "$model" --id_attribute "$id_attr" --feature_type "$feature_type"
-    --mapqMin $mapqMin  --samf "'${firstsamf}','${firstsamf.name}','${firstsamf.ext}','${firstsamf.metadata.bam_index}'"
-    #if $secondsamf.ext != 'data':
-      --samf "'${secondsamf}','${secondsamf.name}','${secondsamf.ext}','${secondsamf.metadata.bam_index}'"
-    #end if
+    --mapqMin $mapqMin  
     #for $s in $samfiles:
-      #if $s.samf.ext != 'data':
-        --samf "'${s.samf}','${s.samf.name}','${s.samf.ext}','${s.samf.metadata.bam_index}'" 
+      #if $s.ext != 'data':
+        --samf "'${s}','${s.name}','${s.ext}','${s.metadata.bam_index}'" 
       #end if
     #end for
     #if $filter_extras:
@@ -58,17 +55,7 @@
         <option value="XS:A">Might be useful for tophat</option>
     </param>   
 
-    <param name="firstsamf" type="data" label="bam/sam file from your history" format="sam,bam" size="100"
-             help="Each sam/bam contributes a column of read counts overlapping the specified gene model contigs" 
-             optional="false"/>
-    <param name="secondsamf" type="data" label="Additional bam/sam file from your history" format="sam,bam" size="100" 
-             help="Each sam/bam contributes a column of read counts overlapping the specified gene model contigs"
-             optional="false"/>
-    <repeat name="samfiles" min="16"
-      title="Specify additional bam/sam file inputs" help="Each sam/bam contributes a column of read counts overlapping the specified gene model contigs">
-        <param name="samf" type="data" label="Additional bam/sam file from your history" format="sam,bam" size="100" 
-             optional="true"/>
-    </repeat>
+    <param name="samfiles" type="data" label="bam/sam file from your history" format="sam,bam" size="100" multiple="true"/>
   </inputs>
   <outputs>
     <data format="tabular" name="outfile" label="${title}_htseqsams2mx.xls" />
@@ -77,8 +64,7 @@
     <test>
       <param name="feature_type" value="exon" />
       <param name="gfffile" value="rn4_chr20_100k.gtf" />
-      <param name="firstsamf" value="rn4chr20test1.bam" ftype="bam"/>
-      <param name="secondsamf" value="rn4chr20test2.bam" ftype="bam"/>
+      <param name="samfiles" value="rn4chr20test1.bam,rn4chr20test2.bam" ftype="bam"/>
       <param name="id_attr" value="gene_name" />
       <param name="model" value="union" />
       <param name="stranded" value="no" />
--- a/test-data/generatetest.sh	Thu Nov 21 18:05:49 2013 -0500
+++ b/test-data/generatetest.sh	Fri Jan 02 03:32:39 2015 -0500
@@ -1,2 +1,3 @@
 #python ../htseqsams2mx.py -g rn4_chr20_100k.gtf -o test.xls --samf "'rn4chr20test1.bam','col1'" --samf "'rn4chr20test2.bam','col2'"
-python ../htseqsams2mx.py -g rn4_chr20_100k.gtf -o htseqsams2mx_test1_out.xls --samf "'rn4chr20test1.bam',''" --samf "'rn4chr20test2.bam',''"
+python ../htseqsams2mx.py -g rn4_chr20_100k.gtf -o htseqsams2mx_test1_out.xls --samf "'rn4chr20test1.bam','test1','bam','rn4chr20test1.bai'" --samf "'rn4chr20test2.bam','test2','bam','rn4chr20test2.bai'"
+
--- a/tool_dependencies.xml	Thu Nov 21 18:05:49 2013 -0500
+++ b/tool_dependencies.xml	Fri Jan 02 03:32:39 2015 -0500
@@ -1,20 +1,20 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="pysam" version="0.7.6">
-        <repository changeset_revision="247e5e5bee87" name="package_pysam_0_7_6" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="247e5e5bee87" name="package_pysam_0_7_6" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="matplotlib" version="1.2.1">
-        <repository changeset_revision="966f29c955b9" name="package_matplotlib_1_2" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
+        <repository changeset_revision="de9c362fb3f2" name="package_matplotlib_1_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="htseq" version="0.5.4p3">
         <install version="1.0">
             <actions>
-                <action type="download_by_url">https://pypi.python.org/packages/source/H/HTSeq/HTSeq-0.5.4p3.tar.gz</action>
+                <action type="download_by_url">https://pypi.python.org/packages/source/H/HTSeq/HTSeq-0.6.1.tar.gz</action>
                 <action type="set_environment_for_install">
-                        <repository changeset_revision="247e5e5bee87" name="package_pysam_0_7_6" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
+                        <repository changeset_revision="247e5e5bee87" name="package_pysam_0_7_6" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
                             <package name="pysam" version="0.7.6" />
                         </repository>
-                        <repository changeset_revision="966f29c955b9" name="package_matplotlib_1_2" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu/">
+                        <repository changeset_revision="de9c362fb3f2" name="package_matplotlib_1_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
                             <package name="matplotlib" version="1.2.1" />
                         </repository>
                 </action>