Mercurial > repos > iracooke > sixframe_translate

annotate sixframe_translate.xml @ 2:e20c4df2bc28 draft default tip

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planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/sixframe-translate/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
author iracooke
date Tue, 20 Oct 2015 20:40:02 -0400
parents 10465e20d9a2
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e20c4df2bc28 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/sixframe-translate/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
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1 <tool id="sixframe_translate" name="Generate 6-frame translation" version="1.1.1">
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2 <description>Translates DNA/RNA to protein</description>
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3 <requirements>
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4 <container type="docker">iracooke/protk-1.4.3</container>
e20c4df2bc28 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/sixframe-translate/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
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5 <requirement type="package" version="1.4.3">protk</requirement>
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6 </requirements>
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7 <stdio>
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8 <exit_code range="1:" level="fatal" description="Failure" />
e20c4df2bc28 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/sixframe-translate/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
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9 </stdio>
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10 <command>
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11 sixframe.rb
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12 $fasta_file
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13 -o $output
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14 $strip_header
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15 $coords
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16 $peptideshaker
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17 --min-len $minlen
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18
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19 #if $gffoutput:
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20 --gff
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21 #end if
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22 </command>
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23 <inputs>
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24 <param name="fasta_file" type="data" format="fasta" label="Uploaded FASTA file" />
e20c4df2bc28 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/sixframe-translate/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
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25 <param name="strip_header" type="boolean" label="Strip header info" help="" truevalue="--strip-header" falsevalue="" />
e20c4df2bc28 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/sixframe-translate/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
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26 <param name="gffoutput" type="boolean" label="Produce gff instead of fasta" help="" truevalue="true" falsevalue="false" />
e20c4df2bc28 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/sixframe-translate/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
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27 <param name="coords" type="boolean" label="Write genomic coordinates" help="" truevalue="--coords" falsevalue="" />
e20c4df2bc28 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/sixframe-translate/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
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28 <param name="peptideshaker" type="boolean" label="Format fasta entries for PeptideShaker" help="" truevalue="--peptideshaker" falsevalue="" />
e20c4df2bc28 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/sixframe-translate/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
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29 <param name="minlen" type="integer" value="20" min="1" label="Minimum Peptide Length"/>
e20c4df2bc28 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/sixframe-translate/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
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30 </inputs>
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31 <outputs>
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32 <data format="fasta" name="output">
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33 <change_format>
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34 <when input="gffoutput" value="true" format="gff3" />
e20c4df2bc28 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/sixframe-translate/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
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35 </change_format>
e20c4df2bc28 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/sixframe-translate/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
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36 </data>
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37 </outputs>
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38 <tests>
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39 <test>
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40 <param name="fasta_file" value="small_genome.fasta" format="fasta"/>
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41 <output name="output" format="fasta">
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42 <assert_contents>
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43 <has_text text="SVQHWFYRFQAGHPRVFCPKNGPRRLW" />
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44 </assert_contents>
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45 </output>
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46 </test>
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47 </tests>
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48 <help>
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49
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50 **What it does**
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51
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52 Generates 6 frame translations suitable for proteogenomics workflows
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53
2
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54 </help>
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55 </tool>