# HG changeset patch
# User fubar
# Date 1370587569 14400
# Node ID 9b2f58a260e9e506564d17b0d15277296d380137
# Parent  b227f5edbe529d93119c5892d5a583c25a987b7a
Uploaded

diff -r b227f5edbe52 -r 9b2f58a260e9 htseq_bams_to_count_matrix/generatetest.sh
--- a/htseq_bams_to_count_matrix/generatetest.sh	Fri Jun 07 01:50:53 2013 -0400
+++ b/htseq_bams_to_count_matrix/generatetest.sh	Fri Jun 07 02:46:09 2013 -0400
@@ -1,1 +1,2 @@
-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 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',''"
diff -r b227f5edbe52 -r 9b2f58a260e9 htseq_bams_to_count_matrix/htseqsams2mx.py
--- a/htseq_bams_to_count_matrix/htseqsams2mx.py	Fri Jun 07 01:50:53 2013 -0400
+++ b/htseq_bams_to_count_matrix/htseqsams2mx.py	Fri Jun 07 02:46:09 2013 -0400
@@ -306,6 +306,8 @@
         assert os.path.isfile(b),'## Supplied input sam file "%s" not found' % b
         sam_filenames.append(b)
         sampName = scolnames[i] # better be unique
+        if sampName == "":
+            sampName = b # for test
         sampName = sampName.replace('#','') # for R
         sampName = sampName.replace('(','') # for R
         sampName = sampName.replace(')','') # for R
diff -r b227f5edbe52 -r 9b2f58a260e9 htseq_bams_to_count_matrix/htseqsams2mx.xml
--- a/htseq_bams_to_count_matrix/htseqsams2mx.xml	Fri Jun 07 01:50:53 2013 -0400
+++ b/htseq_bams_to_count_matrix/htseqsams2mx.xml	Fri Jun 07 02:46:09 2013 -0400
@@ -13,17 +13,19 @@
   <command interpreter="python">
     htseqsams2mx.py -g "$gfffile" -o "$outfile" -m "$model" --id_attribute "$id_attr" --feature_type "$feature_type"
     --samf "'$firstsamf','${firstsamf.name}'"
-    #if secondsamfile:
+    #if $secondsamf:
     --samf "'$secondsamf','${secondsamf.name}'"
     #end if
-    #if thirdsamfile:
+    #if $thirdsamf:
     --samf "'$thirdsamf','${thirdsamf.name}'"
     #end if
-    #if fourthsamfile:
+    #if $fourthsamf:
     --samf "'$fourthsamf','${fourthsamf.name}'"
     #end if
     #for $s in $samfiles:
-    --samf "'${s.samf}','${s.samf.name}'" 
+      #if $s.samf.name:
+        --samf "'${s.samf}','${s.samf.name}'" 
+      #end if
     #end for
   </command>
   <inputs>
@@ -72,16 +74,15 @@
   <tests>
     <test>
       <param name="feature_type" value="exon" />
+      <param name="gfffile" value="rn4_chr20_100k.gtf" />
       <param name="firstsamf" dbkey='rn4' ftype="bam" value="rn4chr20test1.bam" />
-      <param name="firstsamf.name" value="rn4chr20test1.bam" />
       <param name="id_attr" value="gene_id" />
       <param name="model" value="union" />
       <param name="stranded" value="no" />
-      <param name="title" value="htseq test" />
-      <param name="mapqmin" value="0" />
-      <param name="secondsamfile" value="rn4chr20test2.bam" ftype="bam" dbkey="rn4" />
-      <param name="secondsamfile.name" value="rn4chr20test2.bam" />
-      <output name="outfile" file="htseqsams2mx_test1_out.xls" ftype="tabular" lines_diff="30"/>
+      <param name="title" value="htseqtest" />
+      <param name="mapqMin" value="0" />
+      <param name="secondsamf" value="rn4chr20test2.bam" ftype="bam" dbkey="rn4" />
+      <output name="outfile" file="htseqsams2mx_test1_out.xls" ftype="tabular" lines_diff="1"/>
     </test>
   </tests>
   <help>
diff -r b227f5edbe52 -r 9b2f58a260e9 htseq_bams_to_count_matrix/test-data/htseqsams2mx_test1_out.xls
--- a/htseq_bams_to_count_matrix/test-data/htseqsams2mx_test1_out.xls	Fri Jun 07 01:50:53 2013 -0400
+++ b/htseq_bams_to_count_matrix/test-data/htseqsams2mx_test1_out.xls	Fri Jun 07 02:46:09 2013 -0400
@@ -1,4 +1,4 @@
-Contig	col1	col2
+Contig	rn4chr20test1.bam	rn4chr20test2.bam
 Clic2	494	944
 F1M7K0_RAT	3	2
 Tmlhe	164	172