Mercurial > repos > mvdbeek > bam_readtagger
comparison findcluster.xml @ 38:f6311a04a6c9 draft
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6ac744bd9d610990d1d54a2c36ddfca671b15205-dirty
| author | mvdbeek |
|---|---|
| date | Thu, 15 Mar 2018 05:13:22 -0400 |
| parents | 93f7962a3e19 |
| children | 4b1ebfcd0f46 |
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| 37:93f7962a3e19 | 38:f6311a04a6c9 |
|---|---|
| 1 <tool id="findcluster" name="Find clusters of reads" version="0.4.6"> | 1 <tool id="findcluster" name="Find clusters of reads" version="0.4.9"> |
| 2 <description>in bam files</description> | 2 <description>in bam files</description> |
| 3 <macros> | 3 <macros> |
| 4 <import>macros.xml</import> | 4 <import>macros.xml</import> |
| 5 </macros> | 5 </macros> |
| 6 <requirements> | 6 <requirements> |
| 7 <requirement type="package" version="0.4.6">readtagger</requirement> | 7 <requirement type="package" version="0.4.9">readtagger</requirement> |
| 8 </requirements> | 8 </requirements> |
| 9 <version_command>findcluster --version</version_command> | 9 <version_command>findcluster --version</version_command> |
| 10 <command detect_errors="aggressive"><![CDATA[ | 10 <command detect_errors="aggressive"><![CDATA[ |
| 11 #import re | 11 #import re |
| 12 #set sample_name = re.sub('[^\w\-_\.\,]', '_', str( $input.element_identifier)) | 12 #set sample_name = re.sub('[^\w\-_\.\,]', '_', str( $input.element_identifier)) |
| 47 </outputs> | 47 </outputs> |
| 48 <tests> | 48 <tests> |
| 49 <test> | 49 <test> |
| 50 <param name="input" value="extended_and_annotated_roi.bam" ftype="bam"/> | 50 <param name="input" value="extended_and_annotated_roi.bam" ftype="bam"/> |
| 51 <output name="output_bam" file="three_cluster_out.bam" ftype="bam" lines_diff="2"/> | 51 <output name="output_bam" file="three_cluster_out.bam" ftype="bam" lines_diff="2"/> |
| 52 <output name="output_gff" file="three_cluster_out.gff" ftype="gff3" lines_diff="0"/> | 52 <output name="output_gff" file="three_cluster_out.gff" ftype="gff3" lines_diff="0" sort="True"/> |
| 53 </test> | 53 </test> |
| 54 <test> | 54 <test> |
| 55 <param name="input" value="extended_and_annotated_roi.bam" ftype="bam"/> | 55 <param name="input" value="extended_and_annotated_roi.bam" ftype="bam"/> |
| 56 <param name="transposon_source|reference_source_selector" value="history"/> | 56 <param name="transposon_source|reference_source_selector" value="history"/> |
| 57 <param name="transposon_source|ref_file" value="reference.fasta" ftype="fasta"/> | 57 <param name="transposon_source|ref_file" value="reference.fasta" ftype="fasta"/> |