Mercurial > repos > bgruening > crispr_recognition_tool
view crt.xml @ 1:222b7f7b8432 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/crt commit 4241c1d4b05a177bd2c74f5a139f51d4f65e0b55
author | bgruening |
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date | Tue, 13 Jun 2017 08:25:06 -0400 |
parents | db0f5c1cb227 |
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<tool id="crispr_recognition_tool" name="CRISPR Recognition Tool" version="1.2.0"> <description>(CRT)</description> <!-- split_size needs to be 1, because CRT does not support multi fasta file --> <parallelism method="multi" split_inputs="input" split_mode="to_size" split_size="1" merge_outputs="output,output_region" /> <requirements> <requirement type="package" version="1.2">crisper_recognition_tool</requirement> </requirements> <stdio> <exit_code range=":-1" level="fatal" /> <exit_code range="1:" level="fatal" /> </stdio> <command> <![CDATA[ temp_output=\$(mktemp); crt crt -minNR $minNR -minRL $minRL -maxRL $maxRL -minSL $minSL -maxSL $maxSL #if str($searchWL) != 'none': -searchWL $searchWL #end if $input \$temp_output ; python $__tool_directory__/reformat.py \$temp_output $output_region $output ]]> </command> <inputs> <param format="fasta" name="input" type="data" label="Input sequence as FASTA"/> <param name="minNR" type="integer" value="3" label="Minimum number of repeats a CRISPER must have" help="-minNR, default 3"/> <param name="minRL" type="integer" value="19" label="Minimum length of a CRISPER repeated region" help="-minRL, default 19"/> <param name="maxRL" type="integer" value="38" label="Maximum length of a CRISPER repeated region" help="-maxRL, default 38"/> <param name="minSL" type="integer" value="19" label="Minimum length of CRISPER non repeated region" help="or spacer region, -minSL, default 19"/> <param name="maxSL" type="integer" value="48" label="Maximum length of CRISPER non repeated region" help="or spacer region, -maxSL, default 48"/> <param name="searchWL" type="select" label="Length of search window to used to discover CRISPERs" help="-searchWL"> <option value="none" selected="true">default</option> <option value="6">6</option> <option value="7">7</option> <option value="8">8</option> <option value="9">9</option> </param> </inputs> <outputs> <data format="tabular" name="output" label="${tool.name} on ${on_string}" /> <data format="bed" name="output_region" label="${tool.name} on ${on_string} - BED file" /> </outputs> <tests> <test> <param name="input" value="sequence.fasta" ftype="fasta" /> <param name="minNR" value="3" /> <param name="minRL" value="29" /> <param name="maxRL" value="38" /> <param name="minSL" value="19" /> <param name="maxSL" value="48" /> <param name="searchWL" value="none" /> <output name="output" file="crt.tabular" ftype="tabular" /> <output name="output_region" file="crt.bed" ftype="bed" /> </test> </tests> <help> <![CDATA[ **What it does** `CRISPR Recognition Tool <http://www.room220.com/crt/>`_ is a tool for automatic detection of clustered regularly interspaced palindromic repeats (CRISPR). It rapidly and accurately identifies CRISPRs in large DNA strings, such as genomes and metagenomes. **Input** DNA sequence in FASTA format ]]> </help> <citations> <citation type="doi">10.1186/1471-2105-8-209</citation> </citations> </tool>