Mercurial > repos > iracooke > make_protein_decoys

annotate make_decoy.xml @ 2:bd4844c664f2 draft default tip

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planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/make_protein_decoys/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
author iracooke
date Tue, 20 Oct 2015 19:37:19 -0400
parents 354e820eb485
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2
bd4844c664f2 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/make_protein_decoys/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
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1 <tool id="make_decoy" name="Generate protein decoy sequences" version="1.0.1">
bd4844c664f2 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/make_protein_decoys/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
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2 <description>
bd4844c664f2 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/make_protein_decoys/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
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3 Generate random protein sequences with the same AA composition as input sequences
bd4844c664f2 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/make_protein_decoys/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
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4 </description>
bd4844c664f2 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/make_protein_decoys/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
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5 <requirements>
bd4844c664f2 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/make_protein_decoys/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
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6 <container type="docker">iracooke/protk-1.4.3</container>
bd4844c664f2 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/make_protein_decoys/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
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7 <requirement type="package" version="1.4.3">protk</requirement>
bd4844c664f2 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/make_protein_decoys/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
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8 </requirements>
bd4844c664f2 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/make_protein_decoys/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
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9 <stdio>
bd4844c664f2 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/make_protein_decoys/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
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10 <exit_code range="1:" level="fatal" description="Failure" />
bd4844c664f2 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/make_protein_decoys/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
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11 </stdio>
bd4844c664f2 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/make_protein_decoys/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
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12 <command>
bd4844c664f2 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/make_protein_decoys/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
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13 make_decoy.rb $fasta_file -o $output -P $prefix_string $append
bd4844c664f2 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/make_protein_decoys/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
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14 </command>
bd4844c664f2 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/make_protein_decoys/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
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15 <inputs>
bd4844c664f2 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/make_protein_decoys/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
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16 <param name="fasta_file" type="data" format="fasta" label="Fasta file contain protein sequences" />
bd4844c664f2 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/make_protein_decoys/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
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17 <param name="prefix_string" help="Prefix String to use for Decoys" type="text" value="decoy_" label="Prefix String" size="20"/>
bd4844c664f2 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/make_protein_decoys/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 1
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18 <param name="append" type="boolean" label="Append input sequences to the generated sequences" help="" truevalue="--append" falsevalue="" />
bd4844c664f2 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/make_protein_decoys/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 1
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19 </inputs>
bd4844c664f2 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/make_protein_decoys/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
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20 <outputs>
bd4844c664f2 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/make_protein_decoys/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
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21 <data format="fasta" name="output" />
bd4844c664f2 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/make_protein_decoys/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
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22 </outputs>
bd4844c664f2 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/make_protein_decoys/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
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23 <tests>
bd4844c664f2 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/make_protein_decoys/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
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24 <test>
bd4844c664f2 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/make_protein_decoys/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
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25 <param name="fasta_file" value="testdb.fasta" format="fasta"/>
bd4844c664f2 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/make_protein_decoys/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
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26 <output name="output" format="fasta">
bd4844c664f2 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/make_protein_decoys/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
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27 <assert_contents>
bd4844c664f2 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/make_protein_decoys/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
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28 <has_text text="decoy_rp3" />
bd4844c664f2 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/make_protein_decoys/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
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29 </assert_contents>
bd4844c664f2 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/make_protein_decoys/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
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30 </output>
bd4844c664f2 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/make_protein_decoys/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
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31 </test>
bd4844c664f2 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/make_protein_decoys/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
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32 </tests>
bd4844c664f2 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/make_protein_decoys/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
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33 <help>
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34
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35 **What it does**
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36
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37 Generates random protein sequences based on the amino acid composition of a given set of input sequences. To be used for decoy proteomics searches
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38
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39
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bd4844c664f2 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/make_protein_decoys/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
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40 </help>
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41 </tool>