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comparison tools/sample_seqs/sample_seqs.xml @ 7:86710edcec02 draft

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v0.2.5 use <command detect_errors="aggressive"> and other internal changes
author peterjc
date Thu, 11 May 2017 12:20:59 -0400
parents 31f5701cd2e9
children 5f505ed46e16
comparison
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6:31f5701cd2e9 7:86710edcec02
1 <tool id="sample_seqs" name="Sub-sample sequences files" version="0.2.4"> 1 <tool id="sample_seqs" name="Sub-sample sequences files" version="0.2.5">
2 <description>e.g. to reduce coverage</description> 2 <description>e.g. to reduce coverage</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.67">biopython</requirement> 4 <requirement type="package" version="1.67">biopython</requirement>
5 </requirements> 5 </requirements>
6 <stdio> 6 <version_command>
7 <!-- Anything other than zero is an error --> 7 python $__tool_directory__/sample_seqs.py --version
8 <exit_code range="1:" /> 8 </version_command>
9 <exit_code range=":-1" /> 9 <command detect_errors="aggressive">
10 </stdio> 10 python $__tool_directory__/sample_seqs.py -f '$input_file.ext' -i '$input_file' -o '$output_file'
11 <version_command interpreter="python">sample_seqs.py --version</version_command>
12 <command interpreter="python">
13 sample_seqs.py -f "$input_file.ext" -i "$input_file" -o "$output_file"
14 #if str($sampling.type) == "everyNth": 11 #if str($sampling.type) == "everyNth":
15 -n "${sampling.every_n}" 12 -n '${sampling.every_n}'
16 #elif str($sampling.type) == "percentage": 13 #elif str($sampling.type) == "percentage":
17 -p "${sampling.percent}" 14 -p '${sampling.percent}'
18 #else 15 #else
19 -c "${sampling.count}" 16 -c '${sampling.count}'
20 #end if 17 #end if
21 #if $interleaved 18 #if $interleaved
22 --interleaved 19 --interleaved
23 #end if 20 #end if
24 </command> 21 </command>