Mercurial > repos > bgruening > crispr_recognition_tool

annotate crt.xml @ 2:13999e95b2d3 draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/crt commit 4241c1d4b05a177bd2c74f5a139f51d4f65e0b55
author bgruening
date Tue, 13 Jun 2017 10:42:52 -0400
parents 222b7f7b8432
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1 <tool id="crispr_recognition_tool" name="CRISPR Recognition Tool" version="1.2.0">
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2 <description>(CRT)</description>
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3 <!-- split_size needs to be 1, because CRT does not support multi fasta file -->
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4 <parallelism method="multi" split_inputs="input" split_mode="to_size" split_size="1" merge_outputs="output,output_region" />
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5 <requirements>
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6 <requirement type="package" version="1.2">crisper_recognition_tool</requirement>
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7 </requirements>
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8 <stdio>
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9 <exit_code range=":-1" level="fatal" />
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10 <exit_code range="1:" level="fatal" />
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11 </stdio>
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12 <command>
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13 <![CDATA[
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14 temp_output=\$(mktemp);
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15 crt crt
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16 -minNR $minNR
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17 -minRL $minRL
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18 -maxRL $maxRL
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19 -minSL $minSL
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20 -maxSL $maxSL
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21 #if str($searchWL) != 'none':
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22 -searchWL $searchWL
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23 #end if
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24 $input
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25 \$temp_output
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26 ;
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27
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28 python $__tool_directory__/reformat.py \$temp_output $output_region $output
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29 ]]>
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30 </command>
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31 <inputs>
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32 <param format="fasta" name="input" type="data" label="Input sequence as FASTA"/>
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33
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34 <param name="minNR" type="integer" value="3" label="Minimum number of repeats a CRISPER must have" help="-minNR, default 3"/>
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35 <param name="minRL" type="integer" value="19" label="Minimum length of a CRISPER repeated region" help="-minRL, default 19"/>
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36 <param name="maxRL" type="integer" value="38" label="Maximum length of a CRISPER repeated region" help="-maxRL, default 38"/>
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37 <param name="minSL" type="integer" value="19" label="Minimum length of CRISPER non repeated region" help="or spacer region, -minSL, default 19"/>
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38 <param name="maxSL" type="integer" value="48" label="Maximum length of CRISPER non repeated region" help="or spacer region, -maxSL, default 48"/>
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39 <param name="searchWL" type="select" label="Length of search window to used to discover CRISPERs" help="-searchWL">
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40 <option value="none" selected="true">default</option>
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41 <option value="6">6</option>
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42 <option value="7">7</option>
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43 <option value="8">8</option>
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44 <option value="9">9</option>
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45 </param>
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46 </inputs>
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47 <outputs>
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48 <data format="tabular" name="output" label="${tool.name} on ${on_string}" />
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49 <data format="bed" name="output_region" label="${tool.name} on ${on_string} - BED file" />
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50 </outputs>
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51 <tests>
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52 <test>
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53 <param name="input" value="sequence.fasta" ftype="fasta" />
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54 <param name="minNR" value="3" />
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55 <param name="minRL" value="29" />
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56 <param name="maxRL" value="38" />
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57 <param name="minSL" value="19" />
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58 <param name="maxSL" value="48" />
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59 <param name="searchWL" value="none" />
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60 <output name="output" file="crt.tabular" ftype="tabular" />
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61 <output name="output_region" file="crt.bed" ftype="bed" />
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62 </test>
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63 </tests>
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64 <help>
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65 <![CDATA[
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67 **What it does**
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68
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69 `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.
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71 **Input**
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73 DNA sequence in FASTA format
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74
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75 ]]>
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76 </help>
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77 <citations>
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78 <citation type="doi">10.1186/1471-2105-8-209</citation>
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79 </citations>
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80 </tool>
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81