Mercurial > repos > bgruening > minced
annotate minced.xml @ 4:08e4ca411ea6 draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/minced commit edee3afc7d729be9a224d21729bb7490a3761a0e-dirty
| author | bgruening |
|---|---|
| date | Sun, 18 Sep 2016 06:18:17 -0400 |
| parents | 67b57e2f6c7b |
| children |
| rev | line source |
|---|---|
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08e4ca411ea6
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/minced commit edee3afc7d729be9a224d21729bb7490a3761a0e-dirty
bgruening
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changeset
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1 <tool id="minced" name="detect CRISPR sequences" version="0.2.0"> |
| 0 | 2 <description>(minced)</description> |
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08e4ca411ea6
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/minced commit edee3afc7d729be9a224d21729bb7490a3761a0e-dirty
bgruening
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3 <parallelism method="multi" split_inputs="input" split_mode="to_size" split_size="250" merge_outputs="output,output_region,output_ggf_full,output_ggf,output_fasta" /> |
| 0 | 4 <requirements> |
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08e4ca411ea6
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/minced commit edee3afc7d729be9a224d21729bb7490a3761a0e-dirty
bgruening
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5 <requirement type="package" version="0.2.0">minced</requirement> |
| 0 | 6 </requirements> |
| 7 <stdio> | |
| 8 <exit_code range=":-1" level="fatal" /> | |
| 9 <exit_code range="1:" level="fatal" /> | |
| 10 </stdio> | |
| 11 <command> | |
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08e4ca411ea6
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/minced commit edee3afc7d729be9a224d21729bb7490a3761a0e-dirty
bgruening
parents:
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diff
changeset
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12 <![CDATA[ |
| 0 | 13 temp_output=\$(mktemp); |
| 14 minced | |
| 15 -minNR $minNR | |
| 16 -minRL $minRL | |
| 17 -maxRL $maxRL | |
| 18 -minSL $minSL | |
| 19 -maxSL $maxSL | |
| 20 #if str($searchWL) != 'none': | |
| 21 -searchWL $searchWL | |
| 22 #end if | |
| 23 $input | |
| 24 \$temp_output | |
| 25 #if '-spacers' in str($outputs).split(): | |
| 26 -spacers | |
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08e4ca411ea6
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/minced commit edee3afc7d729be9a224d21729bb7490a3761a0e-dirty
bgruening
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27 #end if |
| 0 | 28 #if '-gffFull' in str($outputs).split(): |
| 29 -gffFull | |
| 30 #end if | |
| 31 #if '-gff' in str($outputs).split(): | |
| 32 -gff | |
| 33 #end if | |
| 34 ; | |
| 35 | |
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08e4ca411ea6
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/minced commit edee3afc7d729be9a224d21729bb7490a3761a0e-dirty
bgruening
parents:
3
diff
changeset
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36 python $__tool_directory__/reformat.py \$temp_output results.bed results.tab; |
| 0 | 37 #if '-spacers' in str($outputs).split(): |
| 38 mv \$temp_output'_spacers.fa' $output_fasta; | |
| 39 #end if | |
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08e4ca411ea6
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/minced commit edee3afc7d729be9a224d21729bb7490a3761a0e-dirty
bgruening
parents:
3
diff
changeset
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40 ]]> |
| 0 | 41 </command> |
| 42 <inputs> | |
| 43 <param format="fasta" name="input" type="data" label="Input sequence as FASTA"/> | |
| 44 | |
| 45 <param name="minNR" type="integer" value="3" label="Minimum number of repeats a CRISPER must have"/> | |
| 46 <param name="minRL" type="integer" value="19" label="Minimum length of a CRISPER repeated region"/> | |
| 47 <param name="maxRL" type="integer" value="38" label="Maximum length of a CRISPER repeated region"/> | |
| 48 <param name="minSL" type="integer" value="19" label="Minimum length of CRISPER non repeated region" help="or spacer region"/> | |
| 49 <param name="maxSL" type="integer" value="48" label="Maximum length of CRISPER non repeated region" help="or spacer region"/> | |
| 50 <param name="searchWL" type="select" label="Length of search window to used to discover CRISPERs"> | |
| 51 <option value="none" selected="true">default</option> | |
| 52 <option value="6">6</option> | |
| 53 <option value="7">7</option> | |
| 54 <option value="8">8</option> | |
| 55 <option value="9">9</option> | |
| 56 </param> | |
| 57 | |
| 58 <param name="outputs" type="select" multiple="True" label="Additional output format" help="Please select a output format."> | |
| 59 <option value="-gff">summary results in gff format</option> | |
| 60 <option value="BED" selected="true">summary results in BED format</option> | |
| 61 <option value="-gffFull">detailed results in gff format</option> | |
| 62 <option value="TABULAR" selected="true">detailed results in tabular format</option> | |
| 63 <option value="-spacers">fasta formatted file containing the spacers</option> | |
| 64 <validator type="no_options" message="Please select at least one output file." /> | |
| 65 </param> | |
| 66 | |
| 67 </inputs> | |
| 68 <outputs> | |
| 69 <data format="tabular" name="output" from_work_dir="results.tab" label="${tool.name} on ${on_string}"> | |
| 70 <filter>'TABULAR' in outputs</filter> | |
| 71 </data> | |
| 72 <data format="bed" name="output_region" from_work_dir="results.bed" label="${tool.name} on ${on_string} - BED file"> | |
| 73 <filter>'BED' in outputs</filter> | |
| 74 </data> | |
| 75 <data format="gff3" name="output_ggf_full" from_work_dir="results_full.gff" label="${tool.name} on ${on_string} - GFF file extended"> | |
| 76 <filter>'-gffFull' in outputs</filter> | |
| 77 </data> | |
| 78 <data format="gff3" name="output_gff" from_work_dir="results.gff" label="${tool.name} on ${on_string} - GFF file"> | |
| 79 <filter>'-gff' in outputs</filter> | |
| 80 </data> | |
| 81 <data format="fasta" name="output_fasta" label="${tool.name} on ${on_string} - GFF file"> | |
| 82 <filter>'-spacers' in outputs</filter> | |
| 83 </data> | |
| 84 </outputs> | |
| 85 <tests> | |
| 86 <test> | |
| 87 <param name="input" value="sequence.fasta" ftype="fasta" /> | |
| 88 <param name="minNR" value="3" /> | |
| 89 <param name="minRL" value="29" /> | |
| 90 <param name="maxRL" value="38" /> | |
| 91 <param name="minSL" value="19" /> | |
| 92 <param name="maxSL" value="48" /> | |
| 93 <param name="searchWL" value="none" /> | |
| 94 <output name="output" file="minced.tabular" ftype="tabular" /> | |
| 95 <output name="output_region" file="minced.bed" ftype="bed" /> | |
| 96 </test> | |
| 97 </tests> | |
| 98 <help> | |
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4
08e4ca411ea6
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/minced commit edee3afc7d729be9a224d21729bb7490a3761a0e-dirty
bgruening
parents:
3
diff
changeset
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99 <![CDATA[ |
| 0 | 100 **What it does** |
| 101 | |
| 102 MinCED - Mining CRISPRs in Environmental Datasets | |
| 103 | |
| 104 | |
| 105 MinCED is a program to find Clustered Regularly Interspaced Short Palindromic | |
| 106 Repeats (CRISPRs) in full genomes or environmental datasets such as metagenomes, | |
| 107 in which sequence size can be anywhere from 100 to 800 bp. MinCED runs from the | |
| 108 command-line and was derived from CRT (http://www.room220.com/crt/). | |
| 109 | |
| 110 https://github.com/ctSkennerton/minced | |
| 111 | |
| 112 | |
| 113 If you use this tool in Galaxy, please cite Gruening, BA et al. https://github.com/bgruening/galaxytools | |
| 114 | |
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4
08e4ca411ea6
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/minced commit edee3afc7d729be9a224d21729bb7490a3761a0e-dirty
bgruening
parents:
3
diff
changeset
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115 ]]> |
| 0 | 116 </help> |
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4
08e4ca411ea6
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/minced commit edee3afc7d729be9a224d21729bb7490a3761a0e-dirty
bgruening
parents:
3
diff
changeset
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117 <citations> |
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08e4ca411ea6
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/minced commit edee3afc7d729be9a224d21729bb7490a3761a0e-dirty
bgruening
parents:
3
diff
changeset
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118 <citation type="doi">10.1186/1471-2105-8-209 </citation> |
|
08e4ca411ea6
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/minced commit edee3afc7d729be9a224d21729bb7490a3761a0e-dirty
bgruening
parents:
3
diff
changeset
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119 </citations> |
| 0 | 120 </tool> |
| 121 |