comparison sam_pileup.xml @ 1:e7d863c5c5d6

Update sam_pileup to use the fasta_indexes data table.

0:95612c159681

<tool id="sam_pileup" name="Generate pileup" version="1.1.1">
  <description>from BAM dataset</description>
  <requirements>
    <requirement type="package" version="0.1.16">samtools</requirement>
  </requirements>
  <command interpreter="python">

      --output=$output1
      --ref=$refOrHistory.reference
      #if $refOrHistory.reference == "history":
        --ownFile=$refOrHistory.ownFile
      #else:
        --ownFile="None"
      #end if
       --dbkey=${input1.metadata.dbkey}
       --indexDir=${GALAXY_DATA_INDEX_DIR}
       --bamIndex=${input1.metadata.bam_index}
       --lastCol=$lastCol

        <option value="history">Use one from the history</option>
      </param>
      <when value="indexed">
        <param name="input1" type="data" format="bam" label="Select the BAM file to generate the pileup file for">
           <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="bam" label="Select the BAM file to generate the pileup file for" />
        <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference genome" />

      samtools pileup -M 60 -c -T 0.85 -N 2 -r 0.001 -I 40 -f chr_m.fasta test-data/sam_pileup_in1.bam > sam_pileup_out2.pileup
      chr_m.fasta is the prefix of the index
      -->
      <param name="reference" value="indexed" />
      <param name="input1" value="sam_pileup_in1.bam" ftype="bam" dbkey="equCab2" />
      <param name="lastCol" value="no" />
      <param name="indels" value="no" />
      <param name="mapCap" value="60" />
      <param name="consensus" value="yes" />
      <param name="theta" value="0.85" />

1:e7d863c5c5d6

<tool id="sam_pileup" name="Generate pileup" version="1.1.2">
  <description>from BAM dataset</description>
  <requirements>
    <requirement type="package" version="0.1.16">samtools</requirement>
  </requirements>
  <command interpreter="python">

      --output=$output1
      --ref=$refOrHistory.reference
      #if $refOrHistory.reference == "history":
        --ownFile=$refOrHistory.ownFile
      #else:
        --index=${refOrHistory.index.fields.path}
      #end if
       --dbkey=${input1.metadata.dbkey}
       --indexDir=${GALAXY_DATA_INDEX_DIR}
       --bamIndex=${input1.metadata.bam_index}
       --lastCol=$lastCol

        <option value="history">Use one from the history</option>
      </param>
      <when value="indexed">
        <param name="input1" type="data" format="bam" label="Select the BAM file to generate the pileup file for">
           <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="bam" label="Select the BAM file to generate the pileup file for" />
        <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference genome" />

      samtools pileup -M 60 -c -T 0.85 -N 2 -r 0.001 -I 40 -f chr_m.fasta test-data/sam_pileup_in1.bam > sam_pileup_out2.pileup
      chr_m.fasta is the prefix of the index
      -->
      <param name="reference" value="indexed" />
      <param name="input1" value="sam_pileup_in1.bam" ftype="bam" dbkey="equCab2" />
      <param name="index" value="chr_m" />
      <param name="lastCol" value="no" />
      <param name="indels" value="no" />
      <param name="mapCap" value="60" />
      <param name="consensus" value="yes" />
      <param name="theta" value="0.85" />