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comparison mageck_count.xml @ 3:54f75bda72d5 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 95daf3f97e89989bae687e64cae8b129b3e2b7af
author iuc
date Thu, 19 Apr 2018 05:32:46 -0400
parents 90d6bd926a9b
children c35a871ef887
comparison
equal deleted inserted replaced
2:90d6bd926a9b 3:54f75bda72d5
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="mageck_count" name="MAGeCK count" version="@VERSION@.2" > 2 <tool id="mageck_count" name="MAGeCK count" version="@VERSION@.3" >
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">
11 <command detect_errors="exit_code"><![CDATA[ 11 <command detect_errors="exit_code"><![CDATA[
12 12
13 #if str($reads.format_select) == "files": 13 #if str($reads.format_select) == "files":
14 #import re 14 #import re
15 #set $names = [] 15 #set $names = []
16 #for $i, $sample in enumerate($reads.sample): 16 #set $files = []
17
18 #for $sample in $reads.sample:
19
20 #set name = re.sub('[^\w\-\s]', '_', str($sample.element_identifier))
17 21
18 #if $sample.is_of_type('fastq.gz', 'fastqsanger.gz'): 22 #if $sample.is_of_type('fastq.gz', 'fastqsanger.gz'):
19 ln -s '${sample}' input_${i}.gz && 23 #set infile = $name + ".fq.gz"
20 #set $infile = 'input' + str($i) + '.gz'
21 #elif $sample.is_of_type('fastq'): 24 #elif $sample.is_of_type('fastq'):
22 ln -s '${sample}' input_${i}.fastq && 25 #set infile = $name + ".fq"
23 #set $infile = 'input' + str($i) + 'fastq'
24 #elif $sample.is_of_type('bam'): 26 #elif $sample.is_of_type('bam'):
25 ln -s '${sample}' input_${i}.bam && 27 #set infile = $name + ".bam"
26 #set $infile = 'input' + str($i) + 'bam'
27 #end if 28 #end if
28 #silent $names.append(re.sub('[^\w\-\s]', '_', str($sample.element_identifier))) 29
30 ln -s '${sample}' $infile &&
31
32 #silent $files.append($infile)
33 #silent $names.append($name)
34
29 #end for 35 #end for
30 36 #end if
31 #end if
32
33 37
34 mageck count 38 mageck count
35 39
36 #if str($reads.format_select) == "files": 40 #if str($reads.format_select) == "files":
37 41
38 -l '$reads.sgrna_library_file' 42 -l '$reads.sgrna_library_file'
39 43
40 --fastq input_* 44 --fastq ${ ' '.join( ["'%s'" % $x for $x in $files] ) }
41 45
42 #if $reads.sample_label: 46 #if $reads.sample_label:
43 --sample-label '$reads.sample_label' 47 --sample-label '$reads.sample_label'
44 #else: 48 #else:
45 --sample-label ${ ','.join( $names ) } 49 --sample-label ${ ','.join( ["'%s'" % $x for $x in $names] ) }
46 #end if 50 #end if
47 51
48 #elif str($reads.format_select) == "table": 52 #elif str($reads.format_select) == "table":
49 -k '$reads.counts' 53 -k '$reads.counts'
50 #if '$sgrna_library_file': 54 #if '$sgrna_library_file':
204 <param name="unmappedOpt" value="True" /> 208 <param name="unmappedOpt" value="True" />
205 <param name="pdfreportOpt" value="True" /> 209 <param name="pdfreportOpt" value="True" />
206 <param name="rfilesOpt" value="True" /> 210 <param name="rfilesOpt" value="True" />
207 <param name="logOpt" value="True" /> 211 <param name="logOpt" value="True" />
208 <output name="counts" file="out.count.fastq.txt"/> 212 <output name="counts" file="out.count.fastq.txt"/>
209 <output name="countsummary" file="out.countsummary.txt" compare="sim_size"/> 213 <output name="countsummary" file="out.countsummary.txt" compare="contains"/>
210 <output name="normcounts" file="output.count_normalized.txt"/> 214 <output name="normcounts" file="output.count_normalized.txt"/>
211 <output name="log" file="out.count.log.txt" compare="sim_size"/> 215 <output name="log">
216 <assert_contents>
217 <has_text_matching expression="Welcome to MAGeCK"/>
218 </assert_contents>
219 </output>
212 <output name="unmapped" file="out.count.unmapped.txt" /> 220 <output name="unmapped" file="out.count.unmapped.txt" />
213 <output name="pdfreport" file="out.countsummary.pdf" compare="sim_size" /> 221 <output name="pdfreport" file="out.countsummary.pdf" compare="sim_size" />
214 <output name="rscript" file="out.count.R" /> 222 <output name="rscript" file="out.count.R" />
215 <output name="rnwfile" file="output_countsummary.Rnw" /> 223 <output name="rnwfile">
224 <assert_contents>
225 <has_text_matching expression="This is a template file for Sweave"/>
226 </assert_contents>
227 </output>
216 </test> 228 </test>
217 </tests> 229 </tests>
218 230
219 <help><![CDATA[ 231 <help><![CDATA[
220 .. class:: infomark 232 .. class:: infomark