diff genrich.xml @ 2:8353f3cc03db draft default tip

"planemo upload for repository https://github.com/jsh58/Genrich commit 62a6ec655d7743ce084e45ba02b495e8bd2dc06c"

--- a/genrich.xml	Sat Aug 17 16:24:04 2019 -0400
+++ b/genrich.xml	Thu Aug 29 10:42:38 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="genrich" name="Genrich" version="0.5+galaxy1">
+<tool id="genrich" name="Genrich" version="0.5+galaxy2">
     <description>Detecting sites of genomic enrichment</description>
     <requirements>
         <requirement type="package" version="0.5">genrich</requirement>
@@ -19,7 +19,7 @@
 
 ## Treatment File(s)
 #if str($treatment.t_multi_select) == "Yes":
-    -t ${ ' '.join( [ "'%s'" %  $x for $x in $treatment.input_treatment_file] ) }
+    -t ${ ','.join( [ "'%s'" %  $x for $x in $treatment.input_treatment_file] ) }
 #else
     -t '$treatment.input_treatment_file'
 #end if
@@ -27,7 +27,7 @@
 ## Control File(s)
 #if str($control.c_select) == "Yes":
     #if str($control.c_multiple.c_multi_select) == "Yes":
-        -c ${ ' '.join( [ "'%s'" %  $x for $x in $control.c_multiple.input_control_file] ) }
+        -c ${ ','.join( [ "'%s'" %  $x for $x in $control.c_multiple.input_control_file] ) }
     #else
         -c '$control.c_multiple.input_control_file'
     #end if
@@ -251,6 +251,21 @@
             <output name="out_bedgraph2" ftype="bedgraph" file="CTCF2.bedgraph" compare="contains" lines_diff="1" />
             <output name="out_bed" ftype="bed" file="CTCF.bed" />
         </test>
+        <!-- ChIP Test Data for Pooled Data (Replicates)-->
+        <test expect_num_outputs="4">
+            <param name="input_treatment_file" ftype="bam" value="CTCF_PE_ChIP_chr22.bam,CTCF_PE_ChIP_chr22_2.bam" />
+            <param name="input_control_file" ftype="bam" value="CTCF_PE_CTRL_chr22.bam,CTCF_PE_CTRL_chr22_2.bam" />
+            <param name="c_select" value="Yes" />
+            <param name="t_multi_select" value="Yes" />
+            <param name="c_multi_select" value="Yes" />
+            <param name="bedgraph1" value="True" />
+            <param name="bedgraph2" value="True" />
+            <param name="bed" value="True" />
+            <output name="outfile" ftype="encodepeak" file="Pool.encodepeak" />
+            <output name="out_bedgraph1" ftype="bedgraph" file="Pool1.bedgraph" />
+            <output name="out_bedgraph2" ftype="bedgraph" file="Pool2.bedgraph" compare="contains" lines_diff="2" />
+            <output name="out_bed" ftype="bed" file="Pool.bed" />
+        </test>
     </tests>
     <help><![CDATA[