Mercurial > repos > jasper > pathoscope_map
changeset 2:137a1ee048cc draft default tip
Uploaded
| author | jasper |
|---|---|
| date | Thu, 20 Apr 2017 14:47:12 -0400 |
| parents | 3663119f968a |
| children | |
| files | PathoMap.xml tool-data/pathoscope.loc.sample tool_data_table_conf.xml.sample |
| diffstat | 3 files changed, 70 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PathoMap.xml Thu Apr 20 14:47:12 2017 -0400 @@ -0,0 +1,62 @@ +<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[ + pathoscope MAP + #if str($library.type) == "single" + -U $fastqU + #elif str($library.type) == "paired" + -1 $fastq1 + -2 $fastq2 + #end if + -indexDir $targetAlignPrefixes.fields.path + -targetAlignPrefixes $targetAlignPrefixes + -filterAlignPrefixes $filterAlignPrefixes + ]]> + </command> + <inputs> + <conditional name="library"> + <param name="type" type="select" label="Is this single or paired library" 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="targetAlignPrefixes" type="select" label="targetAlignPrefixes" help="Target Index Prefixes"> + <options from_data_table="pathoscope_indexes"> + <column name="value" index="0"/> + <column name="name" index="0"/> + <column name="path" index="0"/> + </options> + </param> + <param name="filterAlignPrefixes" type="select" label="filterAlignPrefixes" help="Filter Alignment Files Prefixes"> + <options from_data_table="pathoscope_indexes"> + <column name="value" index="0"/> + <column name="name" index="0"/> + <column name="path" index="0"/> + </options> + </param> + </inputs> + <outputs> + </outputs> + <help> + This module will take your reads and map them against a target library. Then it will map the mapping reads +against a filter library. All the reads that map to the filter library with a score equal or greater than the mapping +score to the target library will be discarded. The reads mapping with a better score to the target library will be +used downstream by the PathoID module. + </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>