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comparison print_reads.xml @ 1:64d5adc286bb draft default tip

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planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
author devteam
date Tue, 13 Oct 2015 12:46:26 -0400
parents 6fc6b56b342e
children
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0:6fc6b56b342e 1:64d5adc286bb
1 <tool id="gatk_print_reads" name="Print Reads" version="0.0.1"> 1 <tool id="gatk_print_reads" name="Print Reads" version="0.0.2">
2 <description>from BAM files</description> 2 <description>from BAM files</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.4">gatk</requirement> 4 <requirement type="package" version="1.4">gatk</requirement>
5 <requirement type="package" version="0.1.18">samtools</requirement> 5 <requirement type="package" version="0.1.18">samtools</requirement>
6 </requirements> 6 </requirements>
71 71
72 <param name="number" type="integer" value="-1" label="Print the first n reads from the file, discarding the rest" help="-n,--number &amp;lt;number&amp;gt;" /> 72 <param name="number" type="integer" value="-1" label="Print the first n reads from the file, discarding the rest" help="-n,--number &amp;lt;number&amp;gt;" />
73 <param name="platform" type="text" value="" label="Exclude all reads with this platform from the output" help="-platform,--platform &amp;lt;platform&amp;gt;" /> 73 <param name="platform" type="text" value="" label="Exclude all reads with this platform from the output" help="-platform,--platform &amp;lt;platform&amp;gt;" />
74 <param name="read_group" type="text" value="" label="Exclude all reads with this read group from the output" help="-readGroup,--readGroup &amp;lt;readGroup&amp;gt;" /> 74 <param name="read_group" type="text" value="" label="Exclude all reads with this read group from the output" help="-readGroup,--readGroup &amp;lt;readGroup&amp;gt;" />
75 <repeat name="sample_file_repeat" title="File containing a list of samples to include" help="-sf,--sample_file &amp;lt;sample_file&amp;gt;"> 75 <repeat name="sample_file_repeat" title="File containing a list of samples to include" help="-sf,--sample_file &amp;lt;sample_file&amp;gt;">
76 <param name="input_sample_file" type="data" format="text" label="Sample file" /> 76 <param name="input_sample_file" type="data" format="txt" label="Sample file" />
77 </repeat> 77 </repeat>
78 <repeat name="sample_name_repeat" title="Sample name to be included in the analysis" help="-sn,--sample_name &amp;lt;sample_name&amp;gt;"> 78 <repeat name="sample_name_repeat" title="Sample name to be included in the analysis" help="-sn,--sample_name &amp;lt;sample_name&amp;gt;">
79 <param name="sample_name" type="text" label="Sample name" /> 79 <param name="sample_name" type="text" label="Sample name" />
80 </repeat> 80 </repeat>
81 81
84 </inputs> 84 </inputs>
85 <outputs> 85 <outputs>
86 <data format="bam" name="output_bam" label="${tool.name} on ${on_string} (BAM)" /> 86 <data format="bam" name="output_bam" label="${tool.name} on ${on_string} (BAM)" />
87 <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" /> 87 <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" />
88 </outputs> 88 </outputs>
89 <param name="number" type="integer" value="-1" label="Print the first n reads from the file, discarding the rest" />
90 <param name="platform" type="text" value="" label="Exclude all reads with this platform from the output" />
91 <param name="read_group" type="text" value="" label="Exclude all reads with this read group from the output" />
92 <repeat name="sample_file_repeat" title="File containing a list of samples to include">
93 <param name="input_sample_file" type="data" format="text" label="Sample file" />
94 </repeat>
95 <repeat name="sample_name_repeat" title="Sample name to be included in the analysis">
96 <param name="sample_name" type="text" label="Sample name" />
97 </repeat>
98 <tests> 89 <tests>
99 <test> 90 <test>
100 <param name="reference_source_selector" value="history" /> 91 <param name="reference_source_selector" value="history" />
101 <param name="ref_file" value="phiX.fasta" ftype="fasta" /> 92 <param name="ref_file" value="phiX.fasta" ftype="fasta" />
102 <param name="input_bam" value="gatk/gatk_table_recalibration/gatk_table_recalibration_out_1.bam" ftype="bam" /> 93 <param name="input_bam" value="gatk/gatk_table_recalibration/gatk_table_recalibration_out_1.bam" ftype="bam" />