comparison samtools_mpileup.xml @ 1:dddde948c3e5

Update samtools_mpileup to use the fasta_indexes data table.

0:44a18a94d7a9

<tool id="samtools_mpileup" name="MPileup" version="0.0.1">
  <description>SNP and indel caller</description>
  <requirements>
      <requirement type="package" version="0.1.18">samtools</requirement>
  </requirements>
  <command interpreter="python">samtools_wrapper.py

        <option value="cached">Locally cached</option>
        <option value="history">History</option>
      </param>
      <when value="cached">
        <repeat name="input_bams" title="BAM file" min="1">
            <param name="input_bam" type="data" format="bam" label="BAM file">
              <validator type="unspecified_build" />
              <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 -->
            </param>
        </repeat>
        <param name="ref_file" type="select" label="Using reference genome">
          <options from_data_table="sam_fa_indexes">
            <!-- <filter type="data_meta" key="dbkey" ref="input_bam" column="value"/> does not yet work in a repeat...--> 
          </options>
        </param>
      </when>
      <when value="history"> <!-- FIX ME!!!! -->
        <repeat name="input_bams" title="BAM file" min="1">
            <param name="input_bam" type="data" format="bam" label="BAM file" >
              <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."/>
            </param>
        </repeat>
        <param name="ref_file" type="data" format="fasta" label="Using reference file" />
      </when>
    </conditional>

1:dddde948c3e5

<tool id="samtools_mpileup" name="MPileup" version="0.0.2">
  <description>SNP and indel caller</description>
  <requirements>
      <requirement type="package" version="0.1.18">samtools</requirement>
  </requirements>
  <command interpreter="python">samtools_wrapper.py

        <option value="cached">Locally cached</option>
        <option value="history">History</option>
      </param>
      <when value="cached">
        <repeat name="input_bams" title="BAM file" min="1">
          <param name="input_bam" type="data" format="bam" label="BAM file">
            <validator type="unspecified_build" />
            <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 -->
          </param>
        </repeat>
        <param name="ref_file" type="select" label="Using reference genome">
          <options from_data_table="fasta_indexes">
            <!-- <filter type="data_meta" ref="input_bam" key="dbkey" column="1" /> does not yet work in a repeat...-->
          </options>
        </param>
      </when>
      <when value="history"> <!-- FIX ME!!!! -->
        <repeat name="input_bams" title="BAM file" min="1">
          <param name="input_bam" type="data" format="bam" label="BAM file">
            <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." />
          </param>
        </repeat>
        <param name="ref_file" type="data" format="fasta" label="Using reference file" />
      </when>
    </conditional>