Mercurial > repos > peterjc > samtools_idxstats
comparison tools/samtools_idxstats/samtools_idxstats.xml @ 2:71afa65f444a draft default tip
v0.0.5 Internal changes to command line handling
| author | peterjc |
|---|---|
| date | Tue, 16 May 2017 09:24:18 -0400 |
| parents | 8945bad80f4a |
| children |
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| 1:8945bad80f4a | 2:71afa65f444a |
|---|---|
| 1 <tool id="samtools_idxstats" name="BAM mapping statistics" version="0.0.4"> | 1 <tool id="samtools_idxstats" name="BAM mapping statistics" version="0.0.5"> |
| 2 <description>samtools idxstats</description> | 2 <description>samtools idxstats</description> |
| 3 <requirements> | 3 <requirements> |
| 4 <requirement type="binary">samtools</requirement> | |
| 5 <requirement type="package" version="0.1.19">samtools</requirement> | 4 <requirement type="package" version="0.1.19">samtools</requirement> |
| 6 </requirements> | 5 </requirements> |
| 7 <stdio> | 6 <version_command> |
| 8 <!-- Assume anything other than zero is an error --> | 7 python $__tool_directory__/samtools_idxstats.py --version |
| 9 <exit_code range="1:" /> | 8 </version_command> |
| 10 <exit_code range=":-1" /> | 9 <command detect_errors="aggressive"> |
| 11 </stdio> | 10 python $__tool_directory__/samtools_idxstats.py '$input_bam' '${input_bam.metadata.bam_index}' '$out_tabular' |
| 12 <version_command interpreter="python">samtools_idxstats.py --version</version_command> | 11 </command> |
| 13 <command interpreter="python">samtools_idxstats.py "$input_bam" "${input_bam.metadata.bam_index}" "$out_tabular"</command> | |
| 14 <inputs> | 12 <inputs> |
| 15 <param name="input_bam" type="data" format="bam" label="Input BAM file" /> | 13 <param name="input_bam" type="data" format="bam" label="Input BAM file" /> |
| 16 </inputs> | 14 </inputs> |
| 17 <outputs> | 15 <outputs> |
| 18 <data name="out_tabular" format="tabular" label="$input_bam.name (idxstats)" /> | 16 <data name="out_tabular" format="tabular" label="$input_bam.name (idxstats)" /> |