Mercurial > repos > jasper > pathoscope_map
changeset 0:94d7100ad5d0 draft default tip
Uploaded
| author | jasper |
|---|---|
| date | Sat, 22 Apr 2017 23:47:18 -0400 |
| parents | |
| children | |
| files | PathoMap.xml tool-data/pathoscope.loc.sample tool_data_table_conf.xml.sample |
| diffstat | 3 files changed, 117 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PathoMap.xml Sat Apr 22 23:47:18 2017 -0400 @@ -0,0 +1,77 @@ +<tool id="pathoscope_map" name="Pathoscope Map" version="0.1.0"> + <description> Pathoscope Map </description> + <requirements> + <requirement type="package" version="2.0.6"> pathoscope </requirement> + </requirements> + <command> <![CDATA[ + #from os import listdir + #set path=$targetIndexPrefixes.fields.path.split(',')[0] + #set prefixes=[f for f in listdir(path) if f.endswith(".3.bt2")] + #set targetRefs=str($targetIndexPrefixes) + #set targetR=targetRefs.split(',') + #set p=[] + #for $f in prefixes + #for $t in targetR + #if $t in f + #set p = p + [f[:-6]] + #end if + #end for + #end for + #set target=','.join(p) + pathoscope MAP + #if str($reads.type) == "single" + -U $fastqU + #elif str($reads.type) == "paired" + -1 $fastq1 + -2 $fastq2 + #end if + -indexDir $path + -targetIndexPrefixes $target + -filterIndexPrefixes $filterIndexPrefixes 2>&1 + && mv outalign.sam "$outalign" + && mv pathomap-appendAlign.fq "$pathomap_appendAlign" + ]]> + </command> + <inputs> + <conditional name="reads"> + <param name="type" type="select" label="Is this single or paired reads" help=""> + <option value="single">Single-end</option> + <option value="paired">Paired-end</option> + </param> + <when value="single"> + <param name="fastqU" format="fastqsanger" type="data" label="FASTQ file" help="Input Read Fastq File (Unpaired/Single-end)" /> + </when> + <when value="paired"> + <param name="fastq1" format="fastqsanger" type="data" label="FASTQ file" help="Input Read Fastq File (Unpaired/Single-end)" /> + <param name="fastq2" format="fastqsanger" type="data" label="FASTQ file" help="Input Read Fastq File (Unpaired/Single-end)" /> + </when> + </conditional> + <param name="targetIndexPrefixes" multiple="true" type="select" label="targetIndexPrefixes" help="Target Index Prefixes"> + <options from_data_table="pathoscope_indexes"> + <filter type="sort_by" column="2"/> + <validator type="no_options" message="No indexes are available for the selected input dataset"/> + </options> + </param> + <param name="filterIndexPrefixes" multiple="true" type="select" label="filterIndexPrefixes" help="Filter Index Prefixes"> + <options from_data_table="pathoscope_indexes"> + <filter type="sort_by" column="2"/> + <validator type="no_options" message="No indexes are available for the selected input dataset"/> + </options> + </param> + </inputs> + <outputs> + <data format="sam" name="outalign" label="outalign.sam" /> + <data format="fastqsanger" name="pathomap_appendAlign" label="pathomap_appendAlign.fastq" /> + </outputs> + + <help> + IMPORTANT: The name and the path of the reference database (with bowtie indexed) + should be added to the pathoscope.loc entry. + </help> + <citations> + <citation type="doi">10.1101/gr.150151.112</citation> + <citation type="doi">10.1186/2049-2618-2-33</citation> + <citation type="doi">10.1186/1471-2105-15-262</citation> + <citation type="doi">10.4137/CIN.S13890</citation> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/pathoscope.loc.sample Sat Apr 22 23:47:18 2017 -0400 @@ -0,0 +1,34 @@ +# pathoscope.loc.sample +# This is a *.loc.sample file distributed with Galaxy that enables tools +# to use a directory of indexed data files. This one is for Pathoscope_Map. +# See the wiki: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup +# First create these data files and save them in your own data directory structure. +# Then, create a bowtie_indices.loc file to use those indexes with tools. +# +# The path points to the "basename" for the set, not a specific file. +# It has four text columns seperated by TABS. +# <unique_build_id> <display_name> <file_base_path> +# +# So, for example, if you had hg18 indexes stored in: +# +# /depot/data2/galaxy/hg19/bowtie2/ +# +# containing hg19 genome and hg19.*.bt2 files, such as: +# -rw-rw-r-- 1 james james 914M Feb 10 18:56 hg19canon.fa +# -rw-rw-r-- 1 james james 914M Feb 10 18:56 hg19canon.1.bt2 +# -rw-rw-r-- 1 james james 683M Feb 10 18:56 hg19canon.2.bt2 +# -rw-rw-r-- 1 james james 3.3K Feb 10 16:54 hg19canon.3.bt2 +# -rw-rw-r-- 1 james james 683M Feb 10 16:54 hg19canon.4.bt2 +# -rw-rw-r-- 1 james james 914M Feb 10 20:45 hg19canon.rev.1.bt2 +# -rw-rw-r-- 1 james james 683M Feb 10 20:45 hg19canon.rev.2.bt2 +# +# then the bowtie2_indices.loc entry could look like this: +# +#hg19 hg19 Human (hg19) /depot/data2/galaxy/hg19/bowtie2/hg19canon +# +#Important: put all reference bowtie index into same directory (including both +#target and filter reference botwie index) +# +#More examples: +#ref_prok_rep_genomes prok /depot/data/ref +#ce11 ce /depot/data/ref