comparison bowtie_wrapper.xml @ 2:42c4463baaad draft

Convert tool to use $GALAXY_SLOTS if available.

1:e1c59c194b7b

  </requirements>
  <description></description>
  <parallelism method="basic"></parallelism>
  <command interpreter="python">
    bowtie_wrapper.py
      ## Hackish setting of number of threads
      --threads="4"
      ## Outputs
      --output="${output}"
      #if str( $singlePaired.sPaired ) == "single"
        #if $output_unmapped_reads_l
          --output_unmapped_reads="${output_unmapped_reads_l}"

    <test>
      <!--
      Bowtie command:
      bowtie -q -p 4 -S +sam-nohead chrM_base test-data/bowtie_in2.fastqsanger > bowtie_out6_u.sam
      sort bowtie_out6_u.sam > bowtie_out6.sam
      -p is the number of threads, which is hardcoded above. You need to replace the + with 2 dashes. 
      chrM_base needs to be the base location/name of the index files.
      -->
      <param name="genomeSource" value="indexed" />
      <!-- this is the backwards-compatible "unique value" for this index, not an actual path -->
      <param name="index" value="equCab2chrM" />

      bowtie -q -X 1000 +ff -p 4 -S +sam-nohead -n 2 -e 70 -l 28 +pairtries 100 +maxbts 800 +best +un bowtie_out8_u.fastq phiX_base -1 test-data/bowtie_in5.fastqsanger -2 test-data/bowtie_in6.fastqsanger > bowtie_out7_u.sam
      sort bowtie_out7_u.sam > bowtie_out7.sam
      sort bowtie_out8_u_1.sam > bowtie_out8_1.sam
      sort bowtie_out8_u_2.sam > bowtie_out8_2.sam
      Then also need to modify bowtie_out8_1.sam and bowtie_out8_2.sam so that all @ lines come before sequence lines.
      -p is the number of threads, hardcoded above. You need to replace the + with 2 dashes.
      The two unmapped output files will be named bowtie_out8_1.fastq and bowtie_out8_2.fastq.
      chrM_base is the index files' location/base name. 
      -->
      <param name="genomeSource" value="history" />
      <param name="ownFile" value="phiX.fasta" />

    <test>
      <!--
      Bowtie command:
      bowtie -q -p 4 -S +sam-nohead -n 2 -e 70 -l 28 +maxbts 125 -y -k 1 chrM_base test-data/bowtie_in2.fastqsanger > bowtie_out9_u.sam
      sort bowtie_out9_u.sam > bowtie_out9.sam
      -p is the number of threads, hardcoded above. You need to replace the + with 2 dashes.
      chrM_base is the index files' location/base name. 
      -->
      <param name="genomeSource" value="indexed" />
      <!-- this is the backwards-compatible "unique value" for this index, not an actual path -->
      <param name="index" value="equCab2chrM" />

      <!--
      Bowtie command:
      bowtie-build +offrate 5 +ftabchars 10 +little -f test-data/phiX.fasta phiX_base
      bowtie -q -X 1000 +ff -p 4 -S +sam-nohead phiX_base -1 test-data/bowtie_in5.fastqsanger -2 test-data/bowtie_in6.fastqsanger > bowtie_out10_u.sam
      sort bowtie_out10_u.sam > bowtie_out10.sam
      -p is the number of threads, hardcoded above. You need to replace the + with 2 dashes.
      chrM_base is the index files' location/base name. 
      -->
      <param name="genomeSource" value="history" />
      <param name="ownFile" value="phiX.fasta" />
      <param name="indexSettings" value="indexFull" />

2:42c4463baaad

  </requirements>
  <description></description>
  <parallelism method="basic"></parallelism>
  <command interpreter="python">
    bowtie_wrapper.py
      ## Set number of threads
      --threads="\${GALAXY_SLOTS:-4}"
      ## Outputs
      --output="${output}"
      #if str( $singlePaired.sPaired ) == "single"
        #if $output_unmapped_reads_l
          --output_unmapped_reads="${output_unmapped_reads_l}"

    <test>
      <!--
      Bowtie command:
      bowtie -q -p 4 -S +sam-nohead chrM_base test-data/bowtie_in2.fastqsanger > bowtie_out6_u.sam
      sort bowtie_out6_u.sam > bowtie_out6.sam
      -p is the number of threads. You need to replace the + with 2 dashes. 
      chrM_base needs to be the base location/name of the index files.
      -->
      <param name="genomeSource" value="indexed" />
      <!-- this is the backwards-compatible "unique value" for this index, not an actual path -->
      <param name="index" value="equCab2chrM" />

      bowtie -q -X 1000 +ff -p 4 -S +sam-nohead -n 2 -e 70 -l 28 +pairtries 100 +maxbts 800 +best +un bowtie_out8_u.fastq phiX_base -1 test-data/bowtie_in5.fastqsanger -2 test-data/bowtie_in6.fastqsanger > bowtie_out7_u.sam
      sort bowtie_out7_u.sam > bowtie_out7.sam
      sort bowtie_out8_u_1.sam > bowtie_out8_1.sam
      sort bowtie_out8_u_2.sam > bowtie_out8_2.sam
      Then also need to modify bowtie_out8_1.sam and bowtie_out8_2.sam so that all @ lines come before sequence lines.
      -p is the number of threads. You need to replace the + with 2 dashes.
      The two unmapped output files will be named bowtie_out8_1.fastq and bowtie_out8_2.fastq.
      chrM_base is the index files' location/base name. 
      -->
      <param name="genomeSource" value="history" />
      <param name="ownFile" value="phiX.fasta" />

    <test>
      <!--
      Bowtie command:
      bowtie -q -p 4 -S +sam-nohead -n 2 -e 70 -l 28 +maxbts 125 -y -k 1 chrM_base test-data/bowtie_in2.fastqsanger > bowtie_out9_u.sam
      sort bowtie_out9_u.sam > bowtie_out9.sam
      -p is the number of threads. You need to replace the + with 2 dashes.
      chrM_base is the index files' location/base name. 
      -->
      <param name="genomeSource" value="indexed" />
      <!-- this is the backwards-compatible "unique value" for this index, not an actual path -->
      <param name="index" value="equCab2chrM" />

      <!--
      Bowtie command:
      bowtie-build +offrate 5 +ftabchars 10 +little -f test-data/phiX.fasta phiX_base
      bowtie -q -X 1000 +ff -p 4 -S +sam-nohead phiX_base -1 test-data/bowtie_in5.fastqsanger -2 test-data/bowtie_in6.fastqsanger > bowtie_out10_u.sam
      sort bowtie_out10_u.sam > bowtie_out10.sam
      -p is the number of threads. You need to replace the + with 2 dashes.
      chrM_base is the index files' location/base name. 
      -->
      <param name="genomeSource" value="history" />
      <param name="ownFile" value="phiX.fasta" />
      <param name="indexSettings" value="indexFull" />