comparison lastz_wrapper.xml @ 2:12d4359b7e2f draft

Updated command line format per dev team standards.

1:a36c081e0043

        <requirement type="package" version="1.02.00">lastz</requirement>
    </requirements>
    <description> map short reads against reference sequence</description>
    <command interpreter="python">lastz_wrapper.py
      #if $seq_name.how_to_name=="yes":
        --ref_name=$seq_name.ref_name 
      #end if
      --ref_source=$source.ref_source
      --source_select=$params.source_select
      --out_format=$out_format
      --input2=$input2 
      #if $source.ref_source=="history":
        --input1=$source.input1
        --ref_sequences=$input1.metadata.sequences 
      #else:
        --input1="${source.input1_2bit.fields.path}"
        --ref_sequences="None" 
      #end if
      #if $params.source_select=="pre_set":
        --pre_set_options=${params.pre_set_options}
      #else:
        --strand=$params.strand
        --seed=$params.seed
        --gfextend=$params.gfextend
        --chain=$params.chain
        --transition="$params.transition"
        --O=$params.O
        --E=$params.E
        --X=$params.X
        --Y=$params.Y
        --K=$params.K
        --L=$params.L
        --entropy=$params.entropy 
      #end if
      --identity_min=$min_ident
      --identity_max=$max_ident
      --coverage=$min_cvrg
      --output=$output1
      --unmask=$unmask
      --lastzSeqsFileDir=${GALAXY_DATA_INDEX_DIR}
    </command>
    <inputs>
        <param name="input2" format="fasta" type="data" label="Align sequencing reads in" />
        <conditional name="source">
            <param name="ref_source" type="select" label="Against reference sequences that are">

2:12d4359b7e2f

        <requirement type="package" version="1.02.00">lastz</requirement>
    </requirements>
    <description> map short reads against reference sequence</description>
    <command interpreter="python">lastz_wrapper.py
      #if $seq_name.how_to_name=="yes":
        --ref_name="${seq_name.ref_name}"
      #end if
      --ref_source="${source.ref_source}"
      --source_select="${params.source_select}"
      --out_format="${out_format}"
      --input2="${input2}"
      #if $source.ref_source=="history":
        --input1="${source.input1}"
        --ref_sequences="${input1.metadata.sequences}"
      #else:
        --input1="${source.input1_2bit.fields.path}"
        --ref_sequences="None" 
      #end if
      #if $params.source_select=="pre_set":
        --pre_set_options="${params.pre_set_options}"
      #else:
        --strand="${params.strand}"
        --seed="${params.seed}"
        --gfextend="${params.gfextend}"
        --chain="${params.chain}"
        --transition="${params.transition}"
        --O="${params.O}"
        --E="${params.E}"
        --X="${params.X}"
        --Y="${params.Y}"
        --K="${params.K}"
        --L="${params.L}"
        --entropy="${params.entropy}"
      #end if
      --identity_min="${min_ident}"
      --identity_max="${max_ident}"
      --coverage="${min_cvrg}"
      --output="${output1}"
      --unmask="${unmask}"
      --lastzSeqsFileDir="${GALAXY_DATA_INDEX_DIR}"
    </command>
    <inputs>
        <param name="input2" format="fasta" type="data" label="Align sequencing reads in" />
        <conditional name="source">
            <param name="ref_source" type="select" label="Against reference sequences that are">