Mercurial > repos > devteam > samtools_mpileup
comparison samtools_mpileup.xml @ 1:dddde948c3e5
Update samtools_mpileup to use the fasta_indexes data table.
author | Dave Bouvier <dave@bx.psu.edu> |
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date | Wed, 11 Dec 2013 12:54:32 -0500 |
parents | 44a18a94d7a9 |
children | 973fea5b4bdf |
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0:44a18a94d7a9 | 1:dddde948c3e5 |
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1 <tool id="samtools_mpileup" name="MPileup" version="0.0.1"> | 1 <tool id="samtools_mpileup" name="MPileup" version="0.0.2"> |
2 <description>SNP and indel caller</description> | 2 <description>SNP and indel caller</description> |
3 <requirements> | 3 <requirements> |
4 <requirement type="package" version="0.1.18">samtools</requirement> | 4 <requirement type="package" version="0.1.18">samtools</requirement> |
5 </requirements> | 5 </requirements> |
6 <command interpreter="python">samtools_wrapper.py | 6 <command interpreter="python">samtools_wrapper.py |
57 <option value="cached">Locally cached</option> | 57 <option value="cached">Locally cached</option> |
58 <option value="history">History</option> | 58 <option value="history">History</option> |
59 </param> | 59 </param> |
60 <when value="cached"> | 60 <when value="cached"> |
61 <repeat name="input_bams" title="BAM file" min="1"> | 61 <repeat name="input_bams" title="BAM file" min="1"> |
62 <param name="input_bam" type="data" format="bam" label="BAM file"> | 62 <param name="input_bam" type="data" format="bam" label="BAM file"> |
63 <validator type="unspecified_build" /> | 63 <validator type="unspecified_build" /> |
64 <validator type="dataset_metadata_in_data_table" table_name="sam_fa_indexes" metadata_name="dbkey" metadata_column="value" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select --> | 64 <validator type="dataset_metadata_in_data_table" table_name="fasta_indexes" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select --> |
65 </param> | 65 </param> |
66 </repeat> | 66 </repeat> |
67 <param name="ref_file" type="select" label="Using reference genome"> | 67 <param name="ref_file" type="select" label="Using reference genome"> |
68 <options from_data_table="sam_fa_indexes"> | 68 <options from_data_table="fasta_indexes"> |
69 <!-- <filter type="data_meta" key="dbkey" ref="input_bam" column="value"/> does not yet work in a repeat...--> | 69 <!-- <filter type="data_meta" ref="input_bam" key="dbkey" column="1" /> does not yet work in a repeat...--> |
70 </options> | 70 </options> |
71 </param> | 71 </param> |
72 </when> | 72 </when> |
73 <when value="history"> <!-- FIX ME!!!! --> | 73 <when value="history"> <!-- FIX ME!!!! --> |
74 <repeat name="input_bams" title="BAM file" min="1"> | 74 <repeat name="input_bams" title="BAM file" min="1"> |
75 <param name="input_bam" type="data" format="bam" label="BAM file" > | 75 <param name="input_bam" type="data" format="bam" label="BAM file"> |
76 <validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/> | 76 <validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue." /> |
77 </param> | 77 </param> |
78 </repeat> | 78 </repeat> |
79 <param name="ref_file" type="data" format="fasta" label="Using reference file" /> | 79 <param name="ref_file" type="data" format="fasta" label="Using reference file" /> |
80 </when> | 80 </when> |
81 </conditional> | 81 </conditional> |
82 | 82 |