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comparison slamdunk.xml @ 2:4b677ea9314a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
author iuc
date Mon, 21 Jan 2019 07:34:25 -0500
parents 9dfecde9fa06
children 17f54c2f4b0c
comparison
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1:9dfecde9fa06 2:4b677ea9314a
1 <tool id="slamdunk" name="Slamdunk" version="@TOOL_VERSION@+galaxy1"> 1 <tool id="slamdunk" name="Slamdunk" version="@TOOL_VERSION@+galaxy2">
2 <description>- streamlining SLAM-seq analysis with ultra-high sensitivity</description> 2 <description>- streamlining SLAM-seq analysis with ultra-high sensitivity</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <version_command>slamdunk --version</version_command> 7 <version_command>slamdunk --version</version_command>
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9 #if $reference_source.reference_source_selector == 'history': 9 #import re
10 ln -f -s '$reference_source.ref_file' reference.fa && 10
11 #else: 11 #if $reference_source.reference_source_selector == 'history':
12 ln -f -s '$reference_source.ref_file.fields.path' reference.fa && 12 ln -f -s '$reference_source.ref_file' reference.fa &&
13 #end if 13 #else:
14 slamdunk all -r reference.fa -b '$Reference' -o ./out 14 ln -f -s '$reference_source.ref_file.fields.path' reference.fa &&
15 -n $multimapper.multimappers 15 #end if
16 $multimapper.multimap 16
17 #if $multimapper.filterbed.bedtofilter: 17 mkdir ./fastq &&
18 -fb $multimapper.filterbed.bedtofilter 18 #for $fastq in $reads:
19 #end if 19 #set $fastq_name = re.sub('[^\w\-\.]', '_', str($fastq.element_identifier))
20 -5 $quantseq.trim5 20 ln -s '$fastq' './fastq/${fastq_name}' &&
21 -a $quantseq.maxpolyA 21 #end for
22 $advanced.endtoend 22
23 -mq $advanced.minMQ 23 slamdunk all -r reference.fa -b '$Reference' -o ./out
24 -mi $advanced.minID 24 -n $multimapper.multimappers
25 -nm=$advanced.maxNM 25 $multimapper.multimap
26 -mc $advanced.minCov 26 #if $multimapper.filterbed.bedtofilter:
27 -mv $advanced.minVar 27 -fb $multimapper.filterbed.bedtofilter
28 -mbq $advanced.minBaseQual 28 #end if
29 -rl $readLength 29 -5 $quantseq.trim5
30 -c $covThresh 30 -a $quantseq.maxpolyA
31 '$Reads' 31 $advanced.endtoend
32 -mq $advanced.minMQ
33 -mi $advanced.minID
34 -nm=$advanced.maxNM
35 -mc $advanced.minCov
36 -mv $advanced.minVar
37 -mbq $advanced.minBaseQual
38 -rl $readLength
39 -c $covThresh
40 ./fastq/*
32 ]]></command> 41 ]]></command>
33 <inputs> 42 <inputs>
34 <expand macro="reference_files" /> 43 <expand macro="reference_files" />
35 <param name="Reads" type="data" format="fastqsanger,fastqsanger.gz" label="FASTQ files"/> 44 <param name="reads" type="data" format="fastqsanger,fastqsanger.gz" multiple="True" label="FASTQ files"/>
36 <section name="multimapper" title="Multimapper recovery" 45 <section name="multimapper" title="Multimapper recovery"
37 expanded="false"> 46 expanded="false">
38 <section name="filterbed" 47 <section name="filterbed"
39 title="Use separate 3' UTR bed to filter multimappers." expanded="false"> 48 title="Use separate 3' UTR bed to filter multimappers." expanded="false">
40 <param name="bedtofilter" type="data" format="bed" optional="true" 49 <param name="bedtofilter" type="data" format="bed" optional="true"
84 <param name="readLength" type="integer" min="50" value="50" 93 <param name="readLength" type="integer" min="50" value="50"
85 label="Read length" 94 label="Read length"
86 help="Maximum read length (before trimming)." /> 95 help="Maximum read length (before trimming)." />
87 </inputs> 96 </inputs>
88 <outputs> 97 <outputs>
89 <data name="outputBam" format="bam" from_work_dir="./out/filter/*.bam" label="${tool.name} on ${on_string}: BAM"/> 98 <collection name="outputBam" type="list" label="${tool.name} on ${on_string}: BAM">
90 <data name="outputTsv" format="tabular" from_work_dir="./out/count/*_tcount.tsv" label="${tool.name} on ${on_string}: Count TSV"/> 99 <discover_datasets pattern="(?P&lt;name&gt;.+)\.bam$" format="bam" directory="./out/filter" visible="false" />
91 <data name="outputVcf" format="vcf" from_work_dir="./out/snp/*vcf" label="${tool.name} on ${on_string}: VCF"/> 100 </collection>
101 <collection name="outputTsv" type="list" label="${tool.name} on ${on_string}: Count TSV">
102 <discover_datasets pattern="(?P&lt;name&gt;.+)_tcount.tsv$" format="tabular" directory="./out/count" visible="false" />
103 </collection>
104 <collection name="outputVcf" type="list" label="${tool.name} on ${on_string}: VCF">
105 <discover_datasets pattern="(?P&lt;name&gt;.+)_snp.vcf$" format="vcf" directory="./out/snp" visible="false" />
106 </collection>
92 </outputs> 107 </outputs>
93 <tests> 108 <tests>
94 <test> 109 <test>
95 <!--Ensure default outputs work --> 110 <!--Ensure default outputs work -->
96 <param name="reference_source_selector" value="history" /> 111 <param name="reference_source_selector" value="history" />
97 <param name="ref_file" value="ref.fa" /> 112 <param name="ref_file" value="ref.fa" />
98 <param name="Reference" value="actb.bed" /> 113 <param name="Reference" value="actb.bed" />
99 <param name="Reads" value="reads.fq" /> 114 <param name="reads" value="reads.fq" />
100 <param name="readLength" value="100" /> 115 <param name="readLength" value="100" />
101 <section name="quantseq"> 116 <section name="quantseq">
102 <param name="trim5" value="0" /> 117 <param name="trim5" value="0" />
103 </section> 118 </section>
104 <section name="advanced"> 119 <section name="advanced">
105 <param name="minBaseQual" value="27" /> 120 <param name="minBaseQual" value="27" />
106 </section> 121 </section>
107 <output name="outputBam" ftype="bam" file="reads1.bam" compare="sim_size"/> 122 <output_collection name="outputBam">
108 <output name="outputTsv" ftype="tabular" file="reads_slamdunk_mapped_filtered_tcount.tsv" 123 <element name="reads_slamdunk_mapped_filtered" ftype="bam" file="reads1.bam" compare="sim_size" />
109 lines_diff="2" /> 124 </output_collection>
110 <output name="outputVcf" ftype="vcf" file="reads1_snp.vcf" compare="sim_size"/> 125 <output_collection name="outputTsv">
126 <element name="reads_slamdunk_mapped_filtered" ftype="tabular" file="reads_slamdunk_mapped_filtered_tcount.tsv"
127 lines_diff="2" />
128 </output_collection>
129 <output_collection name="outputVcf">
130 <element name="reads_slamdunk_mapped_filtered" ftype="vcf" file="reads1_snp.vcf" compare="sim_size" />
131 </output_collection>
111 </test> 132 </test>
112 <test> 133 <test>
113 <!--Ensure built-in fasta works --> 134 <!--Ensure built-in fasta works -->
114 <param name="reference_source_selector" value="cached" /> 135 <param name="reference_source_selector" value="cached" />
115 <param name="Reference" value="actb.bed" /> 136 <param name="Reference" value="actb.bed" />
116 <param name="Reads" ftype="fastqsanger" dbkey="hg38" value="reads.fq" /> 137 <param name="reads" ftype="fastqsanger" dbkey="hg38" value="reads.fq" />
117 <param name="readLength" value="100" /> 138 <param name="readLength" value="100" />
118 <section name="quantseq"> 139 <section name="quantseq">
119 <param name="trim5" value="0" /> 140 <param name="trim5" value="0" />
120 </section> 141 </section>
121 <section name="advanced"> 142 <section name="advanced">
122 <param name="minBaseQual" value="27" /> 143 <param name="minBaseQual" value="27" />
123 </section> 144 </section>
124 <output name="outputBam" ftype="bam" file="reads1.bam" compare="sim_size"/> 145 <output_collection name="outputBam">
125 <output name="outputTsv" ftype="tabular" file="reads_slamdunk_mapped_filtered_tcount.tsv" 146 <element name="reads_slamdunk_mapped_filtered" ftype="bam" file="reads1.bam" compare="sim_size" />
126 lines_diff="2" /> 147 </output_collection>
127 <output name="outputVcf" ftype="vcf" file="reads1_snp.vcf" compare="sim_size"/> 148 <output_collection name="outputTsv">
149 <element name="reads_slamdunk_mapped_filtered" ftype="tabular" file="reads_slamdunk_mapped_filtered_tcount.tsv"
150 lines_diff="2" />
151 </output_collection>
152 <output_collection name="outputVcf">
153 <element name="reads_slamdunk_mapped_filtered" ftype="vcf" file="reads1_snp.vcf" compare="sim_size" />
154 </output_collection>
128 </test> 155 </test>
129 </tests> 156 </tests>
130 <help><![CDATA[ 157 <help><![CDATA[
131 SLAM-seq 158 SLAM-seq
132 ======== 159 ========