Mercurial > repos > devteam > print_reads
comparison print_reads.xml @ 1:a8b94864fe35 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gatk/print_reads commit a1517c9d22029095120643bbe2c8fa53754dd2b7
author | devteam |
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date | Wed, 11 Nov 2015 12:44:29 -0500 |
parents | e768f4851646 |
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0:e768f4851646 | 1:a8b94864fe35 |
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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 &lt;number&gt;" /> | 72 <param name="number" type="integer" value="-1" label="Print the first n reads from the file, discarding the rest" help="-n,--number &lt;number&gt;" /> |
73 <param name="platform" type="text" value="" label="Exclude all reads with this platform from the output" help="-platform,--platform &lt;platform&gt;" /> | 73 <param name="platform" type="text" value="" label="Exclude all reads with this platform from the output" help="-platform,--platform &lt;platform&gt;" /> |
74 <param name="read_group" type="text" value="" label="Exclude all reads with this read group from the output" help="-readGroup,--readGroup &lt;readGroup&gt;" /> | 74 <param name="read_group" type="text" value="" label="Exclude all reads with this read group from the output" help="-readGroup,--readGroup &lt;readGroup&gt;" /> |
75 <repeat name="sample_file_repeat" title="File containing a list of samples to include" help="-sf,--sample_file &lt;sample_file&gt;"> | 75 <repeat name="sample_file_repeat" title="File containing a list of samples to include" help="-sf,--sample_file &lt;sample_file&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 &lt;sample_name&gt;"> | 78 <repeat name="sample_name_repeat" title="Sample name to be included in the analysis" help="-sn,--sample_name &lt;sample_name&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" /> |