Mercurial > repos > drosofff > msp_sr_bowtie
diff sRbowtie.xml @ 1:71b072cf5dde draft
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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--- a/sRbowtie.xml Tue May 26 18:36:09 2015 -0400 +++ b/sRbowtie.xml Tue Jun 23 16:58:29 2015 -0400 @@ -1,8 +1,8 @@ -<tool id="bowtieForSmallRNA" name="sRbowtie" version="1.1.0"> +<tool id="bowtieForSmallRNA" name="sRbowtie" version="1.1.1"> <description>for FASTA small reads</description> <requirements> <requirement type="package" version="0.12.7">bowtie</requirement> - <requirement type="package" version="0.1.18">samtools</requirement> + <requirement type="package" version="1.2">samtools</requirement> </requirements> <command interpreter="python"> sRbowtie.py --input $input --input-format $input.extension @@ -55,12 +55,12 @@ </when> </conditional> <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"> - <option select="true" value="tabular">tabular</option> + <option selected="true" value="tabular">tabular</option> <option value="sam">sam</option> <option value="bam">bam</option> </param> <param help="to get aligned and unaligned reads in fasta format" label="additional fasta output" name="additional_fasta" type="select"> - <option select="true" value="No">No</option> + <option selected="true" value="No">No</option> <option value="al">aligned</option> <option value="unal">unaligned</option> <option value="al_and_unal">both aligned and unaligned</option> @@ -105,7 +105,7 @@ <param ftype="fasta" name="input" value="input.fa" /> <param name="v_mismatches" value="1" /> <param name="output_format" value="bam" /> - <output file="output.bam" ftype="bam" lines_diff="4" name="output" /> + <output file="output.bam" ftype="bam" compare="sim_size" delta="1000" name="output" /> </test> <test> <param name="genomeSource" value="history" /> @@ -114,7 +114,7 @@ <param ftype="fastq" name="input" value="input.fastq" /> <param name="v_mismatches" value="1" /> <param name="output_format" value="bam" /> - <output file="output2.bam" ftype="bam" lines_diff="4" name="output" /> + <output file="output2.bam" ftype="bam" compare="sim_size" delta="1000" name="output" /> </test> </tests> <help>