Mercurial > repos > eduardo > download_and_align
changeset 6:18b04f0fb939
Deleted selected files
author | eduardo |
---|---|
date | Fri, 31 Jul 2015 12:22:29 -0400 |
parents | 075e651c7aac |
children | 8accf8976cf7 |
files | download_align.xml tool_data_table_conf.xml.sample |
diffstat | 2 files changed, 0 insertions(+), 61 deletions(-) [+] |
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--- a/download_align.xml Fri Jul 31 12:20:41 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,53 +0,0 @@ -<tool id="download_align" name="Download and align" version="0.0.1"> - <description> Downloads fastq.gz, unzips, trims with cutadapt and alignes to reference</description> - <requirements> - <requirement type="package" version="1.6">cutadapt</requirement> - <requirement type="package" version="2.2.4">bowtie2</requirement> - <requirement type="package" version="0.1.19">samtools</requirement> - </requirements> - <command> - #set index_path = '' - #if str($reference_genome.source) == "history": - echo \${PATH} && bowtie2-build "$reference_genome.own_file" genome && - ln -s "$reference_genome.own_file" genome.fa && - #set index_path = 'genome' - #else: - #set index_path = $reference_genome.index.fields.path - #end if - wget -O - $file | gunzip -c | cutadapt -q 20 - | bowtie2 -q - ## index file path - -x $index_path - -U - | samtools view -b - > $output - </command> - <stdio> - <exit_code range="1:" level="fatal" description="Tool exception" /> - </stdio> - <inputs> - <param format="text" name="file" type="text" label="URL for fastq.gz"/> - <conditional name="reference_genome"> - <param name="source" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options. See `Indexes` section of help below"> - <option value="indexed">Use a built-in genome index</option> - <option value="history">Use a genome from the history and build index</option> - </param> - <when value="indexed"> - <param name="index" type="select" label="Select reference genome" help="If your genome of interest is not listed, contact the Galaxy team"> - <options from_data_table="bowtie2_indexes"> - <filter type="sort_by" column="2"/> - <validator type="no_options" message="No indexes are available for the selected input dataset"/> - </options> - </param> - </when> - <when value="history"> - <param name="own_file" type="data" format="fasta" metadata_name="dbkey" label="Select reference genome" /> - </when> - </conditional> - </inputs> - <outputs> - <data format="bam" name="output" label="${tool.name} on ${on_string}: aligned reads (sorted BAM)" /> - </outputs> - <help> - This tool extracts reads from sra, runs cutdapt and bowtie and outputs a bam file. - - Contact Eduardo Alves at eduardoalves@abdn.ac.uk for support and bug reports. - </help> -</tool>
--- a/tool_data_table_conf.xml.sample Fri Jul 31 12:20:41 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,8 +0,0 @@ -<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc--> -<tables> - <!-- Locations of indexes in the Bowtie2 mapper format --> - <table name="bowtie2_indexes" comment_char="#"> - <columns>value, dbkey, name, path</columns> - <file path="tool-data/bowtie2_indices.loc" /> - </table> -</tables>