Mercurial > repos > iuc > mageck_count
diff mageck_count.xml @ 5:541a5bb7c8c2 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 4478aabdcb10e4787450b1b23944defa7dc38ffe
| author | iuc |
|---|---|
| date | Mon, 04 Jun 2018 10:56:10 -0400 |
| parents | c35a871ef887 |
| children | 9b44a006daa1 |
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--- a/mageck_count.xml Thu Apr 19 18:33:07 2018 -0400 +++ b/mageck_count.xml Mon Jun 04 10:56:10 2018 -0400 @@ -1,5 +1,5 @@ <?xml version="1.0"?> -<tool id="mageck_count" name="MAGeCK count" version="@VERSION@.3" > +<tool id="mageck_count" name="MAGeCK count" version="@VERSION@.4" > <description>- collect sgRNA read counts from read mapping files</description> <macros> <import>mageck_macros.xml</import> @@ -17,7 +17,7 @@ #for $sample in $reads.sample: - #set name = re.sub('[^\w\-\s]', '_', str($sample.element_identifier)) + #set name = re.sub('[^\w\-\.]', '_', str($sample.element_identifier)) #if $sample.is_of_type('fastq.gz', 'fastqsanger.gz'): #set infile = $name + ".fq.gz" @@ -184,14 +184,6 @@ <output name="counts" file="out.count_multi.txt"/> <output name="pdfreport" file="out.countsummary_multi.pdf" compare="sim_size" /> </test> - <!-- Ensure fastq input works --> - <test expect_num_outputs="1"> - <param name="sgrna_library_file" value="demo/demo2/library.txt" ftype="tabular" /> - <param name="format_select" value="files" /> - <param name="sample" value="demo/demo2/test1.fastq" ftype="fastq"/> - <param name="sample_label" value="test1_fastq_gz" /> - <output name="counts" file="out.count.txt"/> - </test> <!-- Ensure BAM input works --> <test expect_num_outputs="1"> <param name="sgrna_library_file" value="demo/demo2/library.txt" ftype="tabular" />