Mercurial > repos > drosofff > msp_sr_bowtie_cascade

comparison sRbowtieCascade.xml @ 1:0dfcb397699e draft

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author drosofff
date Mon, 13 Apr 2015 12:31:00 -0400
parents ecb041b49cd7
children 0052d1dd31df
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0:ecb041b49cd7 1:0dfcb397699e
1 <tool id="sRbowtie_cascade" name="Annotate smRNA datasets" version="1.0.0"> 1 <tool id="sRbowtie_cascade" name="Annotate smRNA datasets" version="1.0.1">
2 <description>Using iterative sRbowtie Alignments</description> 2 <description>Using iterative sRbowtie Alignments</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.12.7">bowtie</requirement> 4 <requirement type="package" version="0.12.7">bowtie</requirement>
5 </requirements> 5 </requirements>
6 <parallelism method="basic"></parallelism>
7 <command interpreter="python"> sRbowtieCascade.py --output $output 6 <command interpreter="python"> sRbowtieCascade.py --output $output
8 --num-threads \${GALAXY_SLOTS:-4} ## number of processors to be handled by bowtie 7 --num-threads \${GALAXY_SLOTS:-4} ## number of processors to be handled by bowtie
9 --mismatch $mismatches 8 --mismatch $mismatches
10 --input 9 --input
11 #for $i in $input: 10 #for $i in $input:
92 </inputs> 91 </inputs>
93 <outputs> 92 <outputs>
94 <data format="tabular" name="output" label="Cascade Annotation Analysis"/> 93 <data format="tabular" name="output" label="Cascade Annotation Analysis"/>
95 </outputs> 94 </outputs>
96 95
97 <test>
98 </test>
99 96
97 <tests>
98 <test>
99 <param name="input" value ="sample1.fa,sample2.fa,sample3.fa" ftype="fasta" />
100 <param name="genomeSource" value="history" />
101 <param name="ownFile" value ="dmel-2L-r6.04.fasta" ftype="fasta" />
102 <param name="AdditionalQueries_0|refGenomeSource|genomeSource" value="history"/>
103 <param name="AdditionalQueries_0|refGenomeSource|ownFile" value="dme_miR21_hairpin.fa" ftype="fasta" />
104 <param name="AdditionalQueries_1|refGenomeSource|genomeSource" value="history"/>
105 <param name="AdditionalQueries_1|refGenomeSource|ownFile" value="Ensembl_transposon_set.fa" ftype="fasta" />
106 <output name="output" ftype="tabular" file="Cascade_Annotation_Analysis.tab" />
107 </test>
108 </tests>
100 <help> 109 <help>
101 110
102 **Intro** 111 **Intro**
103 112
104 Bowtie_ is a short read aligner designed to be ultrafast and memory-efficient. 113 Bowtie_ is a short read aligner designed to be ultrafast and memory-efficient.