Mercurial > repos > drosofff > msp_sr_bowtie

comparison sRbowtie.xml @ 1:71b072cf5dde draft

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planemo upload for repository https://bitbucket.org/drosofff/gedtools/
author drosofff
date Tue, 23 Jun 2015 16:58:29 -0400
parents e8bdae1a2bdc
children c1bfa227bbb6
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0:e8bdae1a2bdc 1:71b072cf5dde
1 <tool id="bowtieForSmallRNA" name="sRbowtie" version="1.1.0"> 1 <tool id="bowtieForSmallRNA" name="sRbowtie" version="1.1.1">
2 <description>for FASTA small reads</description> 2 <description>for FASTA small reads</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 <requirement type="package" version="0.1.18">samtools</requirement> 5 <requirement type="package" version="1.2">samtools</requirement>
6 </requirements> 6 </requirements>
7 <command interpreter="python"> sRbowtie.py --input $input 7 <command interpreter="python"> sRbowtie.py --input $input
8 --input-format $input.extension 8 --input-format $input.extension
9 --method $method 9 --method $method
10 --v-mismatches $v_mismatches 10 --v-mismatches $v_mismatches
53 <when value="history"> 53 <when value="history">
54 <param format="fasta" label="Select a fasta file, to serve as index reference" name="ownFile" type="data" /> 54 <param format="fasta" label="Select a fasta file, to serve as index reference" name="ownFile" type="data" />
55 </when> 55 </when>
56 </conditional> 56 </conditional>
57 <param help="Note that the BAM will be viewable in trackster only if you choose a full genome referenced for Trackster usage. see the doc below" label="Select output format" name="output_format" type="select"> 57 <param help="Note that the BAM will be viewable in trackster only if you choose a full genome referenced for Trackster usage. see the doc below" label="Select output format" name="output_format" type="select">
58 <option select="true" value="tabular">tabular</option> 58 <option selected="true" value="tabular">tabular</option>
59 <option value="sam">sam</option> 59 <option value="sam">sam</option>
60 <option value="bam">bam</option> 60 <option value="bam">bam</option>
61 </param> 61 </param>
62 <param help="to get aligned and unaligned reads in fasta format" label="additional fasta output" name="additional_fasta" type="select"> 62 <param help="to get aligned and unaligned reads in fasta format" label="additional fasta output" name="additional_fasta" type="select">
63 <option select="true" value="No">No</option> 63 <option selected="true" value="No">No</option>
64 <option value="al">aligned</option> 64 <option value="al">aligned</option>
65 <option value="unal">unaligned</option> 65 <option value="unal">unaligned</option>
66 <option value="al_and_unal">both aligned and unaligned</option> 66 <option value="al_and_unal">both aligned and unaligned</option>
67 </param> 67 </param>
68 </inputs> 68 </inputs>
103 <param ftype="fasta" name="ownFile" value="297_reference.fa" /> 103 <param ftype="fasta" name="ownFile" value="297_reference.fa" />
104 <param name="method" value="unique" /> 104 <param name="method" value="unique" />
105 <param ftype="fasta" name="input" value="input.fa" /> 105 <param ftype="fasta" name="input" value="input.fa" />
106 <param name="v_mismatches" value="1" /> 106 <param name="v_mismatches" value="1" />
107 <param name="output_format" value="bam" /> 107 <param name="output_format" value="bam" />
108 <output file="output.bam" ftype="bam" lines_diff="4" name="output" /> 108 <output file="output.bam" ftype="bam" compare="sim_size" delta="1000" name="output" />
109 </test> 109 </test>
110 <test> 110 <test>
111 <param name="genomeSource" value="history" /> 111 <param name="genomeSource" value="history" />
112 <param ftype="fasta" name="ownFile" value="297_reference.fa" /> 112 <param ftype="fasta" name="ownFile" value="297_reference.fa" />
113 <param name="method" value="unique" /> 113 <param name="method" value="unique" />
114 <param ftype="fastq" name="input" value="input.fastq" /> 114 <param ftype="fastq" name="input" value="input.fastq" />
115 <param name="v_mismatches" value="1" /> 115 <param name="v_mismatches" value="1" />
116 <param name="output_format" value="bam" /> 116 <param name="output_format" value="bam" />
117 <output file="output2.bam" ftype="bam" lines_diff="4" name="output" /> 117 <output file="output2.bam" ftype="bam" compare="sim_size" delta="1000" name="output" />
118 </test> 118 </test>
119 </tests> 119 </tests>
120 <help> 120 <help>
121 121
122 **What it does** 122 **What it does**