comparison sopra_wpc.xml @ 2:87ffe493b6c1 draft default tip

Use GALAXY_SLOTS for multithreading in Bowtie. Create symlinks instead of copying files. Specify in help that Bowtie is used to align the reads to the contigs. Add readme.rst .

1:d180348fe9db

<tool id="sopra_wpc" name="SOPRA with prebuilt contigs" version="0.1">
  <description>for Illumina workflow</description>
  <requirements>
    <requirement type="package" version="1.4.6">sopra</requirement>
    <requirement type="package" version="1.0.0">bowtie</requirement>
  </requirements>
  <command interpreter="python">
    sopra_wpc.py
    #for $cr in $contigs_repeat
      --contigs ${cr.contigs_file}
    #end for
    #for $mr in $mate_repeat
      --mate ${mr.mate_file}

    <data format="txt" name="logfile" label="${tool.name} on ${on_string}: log"/>
  </outputs>
  <help>
**What it does**

SOPRA is an assembly tool for mate pair/paired-end data generated by high-throughput sequencing technologies, e.g. Illumina and SOLiD platforms.

The input paired-end FASTA file can be obtained with:
FR reads -> *FASTQ interlacer on paired end reads* followed by *FASTQ to FASTA* converter
RF reads -> *Reverse-Complement*, *FASTQ interlacer on paired end reads* followed by *FASTQ to FASTA* converter

2:87ffe493b6c1

<tool id="sopra_wpc" name="SOPRA with prebuilt contigs" version="0.1">
  <description>for Illumina libraries</description>
  <requirements>
    <requirement type="package" version="1.4.6">sopra</requirement>
    <requirement type="package" version="1.0.0">bowtie</requirement>
  </requirements>
  <command interpreter="python">
    sopra_wpc.py -p \${GALAXY_SLOTS:-1}
    #for $cr in $contigs_repeat
      --contigs ${cr.contigs_file}
    #end for
    #for $mr in $mate_repeat
      --mate ${mr.mate_file}

    <data format="txt" name="logfile" label="${tool.name} on ${on_string}: log"/>
  </outputs>
  <help>
**What it does**

SOPRA is a scaffold assembly tool for paired-end/mate pair data generated by high-throughput sequencing technologies, e.g. Illumina and SOLiD platforms. This wrapper currently supports only Illumina paired-end data.

Bowtie is used to align the reads to the contigs.

The input paired-end FASTA file can be obtained with:
FR reads -> *FASTQ interlacer on paired end reads* followed by *FASTQ to FASTA* converter
RF reads -> *Reverse-Complement*, *FASTQ interlacer on paired end reads* followed by *FASTQ to FASTA* converter