Mercurial > repos > iuc > genrich
diff genrich.xml @ 2:8353f3cc03db draft default tip
"planemo upload for repository https://github.com/jsh58/Genrich commit 62a6ec655d7743ce084e45ba02b495e8bd2dc06c"
| author | iuc |
|---|---|
| date | Thu, 29 Aug 2019 10:42:38 -0400 |
| parents | db50f51a2952 |
| children |
line wrap: on
line diff
--- 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[