Mercurial > repos > iuc > mageck_count

comparison mageck_count.xml @ 5:541a5bb7c8c2 draft

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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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4:c35a871ef887 5:541a5bb7c8c2
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="mageck_count" name="MAGeCK count" version="@VERSION@.3" > 2 <tool id="mageck_count" name="MAGeCK count" version="@VERSION@.4" >
3 <description>- collect sgRNA read counts from read mapping files</description> 3 <description>- collect sgRNA read counts from read mapping files</description>
4 <macros> 4 <macros>
5 <import>mageck_macros.xml</import> 5 <import>mageck_macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements"> 7 <expand macro="requirements">
15 #set $names = [] 15 #set $names = []
16 #set $files = [] 16 #set $files = []
17 17
18 #for $sample in $reads.sample: 18 #for $sample in $reads.sample:
19 19
20 #set name = re.sub('[^\w\-\s]', '_', str($sample.element_identifier)) 20 #set name = re.sub('[^\w\-\.]', '_', str($sample.element_identifier))
21 21
22 #if $sample.is_of_type('fastq.gz', 'fastqsanger.gz'): 22 #if $sample.is_of_type('fastq.gz', 'fastqsanger.gz'):
23 #set infile = $name + ".fq.gz" 23 #set infile = $name + ".fq.gz"
24 #elif $sample.is_of_type('fastq'): 24 #elif $sample.is_of_type('fastq'):
25 #set infile = $name + ".fq" 25 #set infile = $name + ".fq"
181 <param name="format_select" value="files" /> 181 <param name="format_select" value="files" />
182 <param name="sample" value="test1.fastq.gz,test2.fastq.gz" ftype="fastq.gz"/> 182 <param name="sample" value="test1.fastq.gz,test2.fastq.gz" ftype="fastq.gz"/>
183 <param name="pdfreportOpt" value="True" /> 183 <param name="pdfreportOpt" value="True" />
184 <output name="counts" file="out.count_multi.txt"/> 184 <output name="counts" file="out.count_multi.txt"/>
185 <output name="pdfreport" file="out.countsummary_multi.pdf" compare="sim_size" /> 185 <output name="pdfreport" file="out.countsummary_multi.pdf" compare="sim_size" />
186 </test>
187 <!-- Ensure fastq input works -->
188 <test expect_num_outputs="1">
189 <param name="sgrna_library_file" value="demo/demo2/library.txt" ftype="tabular" />
190 <param name="format_select" value="files" />
191 <param name="sample" value="demo/demo2/test1.fastq" ftype="fastq"/>
192 <param name="sample_label" value="test1_fastq_gz" />
193 <output name="counts" file="out.count.txt"/>
194 </test> 186 </test>
195 <!-- Ensure BAM input works --> 187 <!-- Ensure BAM input works -->
196 <test expect_num_outputs="1"> 188 <test expect_num_outputs="1">
197 <param name="sgrna_library_file" value="demo/demo2/library.txt" ftype="tabular" /> 189 <param name="sgrna_library_file" value="demo/demo2/library.txt" ftype="tabular" />
198 <param name="format_select" value="files" /> 190 <param name="format_select" value="files" />