comparison sam_to_bam.xml @ 1:93f2e3337a33

Update sam_to_bam to use the fasta_indexes data table.

0:30fdbaccb96b

<tool id="sam_to_bam" name="SAM-to-BAM" version="1.1.2">
  <description>converts SAM format to BAM format</description>
  <requirements>
    <requirement type="package" version="0.1.18">samtools</requirement>
  </requirements>
  <command interpreter="python">
    sam_to_bam.py
      --input1=$source.input1
      #if $source.index_source == "history":
        --dbkey=${ref_file.metadata.dbkey} 
        --ref_file=$source.ref_file
      #else
        --dbkey=${input1.metadata.dbkey} 
      #end if
      --output1=$output1
      --index_dir=${GALAXY_DATA_INDEX_DIR}
  </command>
  <inputs>
    <conditional name="source">
      <param name="index_source" type="select" label="Choose the source for the reference list">
        <option value="cached">Locally cached</option>
        <option value="history">History</option>
      </param>
      <when value="cached">
        <param name="input1" type="data" format="sam" metadata_name="dbkey" label="SAM File to Convert">
           <validator type="unspecified_build" />
           <validator type="dataset_metadata_in_file" filename="sam_fa_indices.loc" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." line_startswith="index" />
        </param>
      </when>
      <when value="history">
        <param name="input1" type="data" format="sam" label="Convert SAM file" />
        <param name="ref_file" type="data" format="fasta" metadata_name="dbkey" label="Using reference file" />
      </when>
    </conditional>
  </inputs>
  <outputs>

      chr_m.fasta is the reference file and the index chr_m.fasta.fai 
      these should be in the same directory, and chrM is from equCab2
      -->
      <param name="index_source" value="cached" />
      <param name="input1" value="sam_to_bam_in1.sam" ftype="sam" dbkey="chrM" />
      <output name="output1" file="sam_to_bam_out2.bam" ftype="bam" />
    </test>
  </tests>
  <help>

1:93f2e3337a33

<tool id="sam_to_bam" name="SAM-to-BAM" version="1.1.3">
  <description>converts SAM format to BAM format</description>
  <requirements>
    <requirement type="package" version="0.1.18">samtools</requirement>
  </requirements>
  <command interpreter="python">
    sam_to_bam.py
      --input1=$source.input1
      #if $source.index_source == "history":
        --ref_file=$source.ref_file
      #else
        --index=${source.index.fields.path}
      #end if
      --output1=$output1
  </command>
  <inputs>
    <conditional name="source">
      <param name="index_source" type="select" label="Choose the source for the reference list">
        <option value="cached">Locally cached</option>
        <option value="history">History</option>
      </param>
      <when value="cached">
        <param name="input1" type="data" format="sam" metadata_name="dbkey" label="SAM file to convert">
          <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." />
        </param>
        <param name="index" type="select" label="Using reference genome">
          <options from_data_table="fasta_indexes">
            <filter type="data_meta" ref="input1" key="dbkey" column="1" />
            <validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset" />
          </options>
        </param>
      </when>
      <when value="history">
        <param name="input1" type="data" format="sam" label="SAM file to convert" />
        <param name="ref_file" type="data" format="fasta" metadata_name="dbkey" label="Using reference file" />
      </when>
    </conditional>
  </inputs>
  <outputs>

      chr_m.fasta is the reference file and the index chr_m.fasta.fai 
      these should be in the same directory, and chrM is from equCab2
      -->
      <param name="index_source" value="cached" />
      <param name="input1" value="sam_to_bam_in1.sam" ftype="sam" dbkey="chrM" />
      <param name="index" value="chr_m" />
      <output name="output1" file="sam_to_bam_out2.bam" ftype="bam" />
    </test>
  </tests>
  <help>