Mercurial > repos > iuc > bam_to_scidx
comparison bam_to_scidx.xml @ 1:ebbf2a6a4c55 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit f33b04533bca91242b8a0a4077e1d593f5a874e0
author | iuc |
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date | Tue, 19 Apr 2016 18:10:09 -0400 |
parents | 741b8af6386c |
children | bd79c4d39af0 |
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0:741b8af6386c | 1:ebbf2a6a4c55 |
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1 <tool id="bam_to_scidx" name="Convert BAM to ScIdx" version="1.0.0"> | 1 <tool id="bam_to_scidx" name="Convert BAM to ScIdx" version="1.0.0"> |
2 <description></description> | 2 <description></description> |
3 <requirements> | |
4 <requirement type="package" version="8.0.45">java-jdk</requirement> | |
5 </requirements> | |
3 <command> | 6 <command> |
4 <![CDATA[ | 7 <![CDATA[ |
5 ln -f -s "${input_bam.metadata.bam_index}" "${input_bam}.bai" && | 8 ln -f -s "${input_bam.metadata.bam_index}" "${input_bam}.bai" && |
6 java -jar $__tool_directory__/BAMtoscIDX.jar -b "$input_bam" -i "${input_bam}.bai" -p $require_proper_mate_pairing -r $read -m $min_insert_size -M $max_insert_size -o "$output" 1>/dev/null | 9 java -jar $__tool_directory__/BAMtoscIDX.jar -b "$input_bam" -i "${input_bam}.bai" -p $require_proper_mate_pairing -r $read -m $min_insert_size -M $max_insert_size -o "$output" 1>/dev/null |
7 ]]> | 10 ]]> |
26 <tests> | 29 <tests> |
27 <test> | 30 <test> |
28 <param name="input_bam" value="input.bam" ftype="bam" /> | 31 <param name="input_bam" value="input.bam" ftype="bam" /> |
29 <param name="require_proper_mate_pairing" value="1" /> | 32 <param name="require_proper_mate_pairing" value="1" /> |
30 <param name="read" value="0" /> | 33 <param name="read" value="0" /> |
31 <output name="output" file="output.scidx" lines_diff="1" ftype="scidx" /> | 34 <output name="output" file="output.scidx" lines_diff="1" ftype="scidx" compare="contains" /> |
32 </test> | 35 </test> |
33 </tests> | 36 </tests> |
34 <help> | 37 <help> |
35 | 38 |
36 **What it does** | 39 **What it does** |