Mercurial > repos > galaxyp > uniprotxml_downloader
annotate uniprotxml_downloader.xml @ 1:fc8c4bd28681 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
| author | galaxyp |
|---|---|
| date | Wed, 07 Dec 2016 16:44:14 -0500 |
| parents | 0bd2688166a5 |
| children | e1abc9a35c64 |
| rev | line source |
|---|---|
|
1
fc8c4bd28681
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
0
diff
changeset
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1 <tool id="uniprotxml_downloader" name="UniProtXML Download" version="1.0.1"> |
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0bd2688166a5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
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changeset
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2 <description>proteome</description> |
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0bd2688166a5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
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changeset
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3 <requirements> |
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1
fc8c4bd28681
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
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diff
changeset
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4 <requirement type="package" version="2.7.12">python</requirement> |
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0
0bd2688166a5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
diff
changeset
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5 </requirements> |
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0bd2688166a5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
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changeset
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6 <stdio> |
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0bd2688166a5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
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changeset
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7 <exit_code range="1:" level="fatal" description="Error downloading proteome." /> |
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0bd2688166a5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
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changeset
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8 </stdio> |
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1
fc8c4bd28681
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
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diff
changeset
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9 <command> |
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0
0bd2688166a5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
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changeset
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10 <![CDATA[ |
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1
fc8c4bd28681
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
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changeset
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11 python '$__tool_directory__/uniprotxml_downloader.py' |
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fc8c4bd28681
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
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changeset
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12 -v |
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fc8c4bd28681
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
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13 #if $taxid.choice == 'common': |
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fc8c4bd28681
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
0
diff
changeset
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14 --taxon '$taxid.organism' |
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fc8c4bd28681
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
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diff
changeset
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15 #if $taxid.reviewed: |
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fc8c4bd28681
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
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16 --reviewed=$taxid.reviewed |
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fc8c4bd28681
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
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17 #end if |
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fc8c4bd28681
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
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diff
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18 #else: |
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fc8c4bd28681
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
0
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19 #for id in $taxid.taxons.split(','): |
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fc8c4bd28681
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
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20 -t $id |
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fc8c4bd28681
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
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diff
changeset
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21 #end for |
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fc8c4bd28681
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
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changeset
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22 #end if |
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fc8c4bd28681
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
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changeset
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23 --output="${proteome}" |
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0
0bd2688166a5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
diff
changeset
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24 ]]> |
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0bd2688166a5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
diff
changeset
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25 </command> |
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0bd2688166a5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
diff
changeset
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26 <inputs> |
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0bd2688166a5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
diff
changeset
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27 <conditional name="taxid"> |
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0bd2688166a5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
diff
changeset
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28 <param name="choice" type="select" label="Select"> |
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0bd2688166a5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
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changeset
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29 <option value="common">A Common Organism</option> |
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0bd2688166a5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
diff
changeset
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30 <option value="taxids">By Organism IDs</option> |
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0bd2688166a5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
diff
changeset
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31 </param> |
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0bd2688166a5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
diff
changeset
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32 <when value="common"> |
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0bd2688166a5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
diff
changeset
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33 <param name="organism" type="select" label="Common Organisms" |
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0bd2688166a5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
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34 help="select species for protein database"> |
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0bd2688166a5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
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changeset
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35 <options from_file="uniprot_taxons.loc"> |
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0bd2688166a5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
diff
changeset
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36 <column name="name" index="0" /> |
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0bd2688166a5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
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changeset
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37 <column name="value" index="1" /> |
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0bd2688166a5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
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changeset
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38 </options> |
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0bd2688166a5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
diff
changeset
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39 </param> |
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0bd2688166a5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
diff
changeset
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40 <param name="reviewed" type="select" label="filter by reviewed status" optional="true"> |
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0bd2688166a5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
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41 <help><![CDATA[ |
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0bd2688166a5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
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changeset
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42 UniProtKB/TrEMBL (unreviewed)is a large, automatically annotated database that may contain |
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0bd2688166a5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
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changeset
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43 redundant sequences, but there is a higher chance peptides will be identified. |
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0bd2688166a5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
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44 UniProtKB/Swiss-Prot (reviewed) is a smaller, manually annotated database with |
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0bd2688166a5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
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45 less of a chance peptides will be identified but less sequence redundancy |
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0bd2688166a5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
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46 ]]> |
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0bd2688166a5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
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47 </help> |
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0bd2688166a5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
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48 <option value="yes">UniProtKB/Swiss-Prot (reviewed only)</option> |
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0bd2688166a5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
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49 <option value="no">UniProtKB/TrEMBL (unreviewed only)</option> |
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0bd2688166a5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
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50 </param> |
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0bd2688166a5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
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51 </when> |
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0bd2688166a5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
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52 <when value="taxids"> |
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0bd2688166a5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
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53 <param name="taxons" type="text" label="NCBI taxon IDs" |
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0bd2688166a5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
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54 help="Enter one or more Organsim IDs (separated by commas) from http://www.uniprot.org/proteomes/"> |
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0bd2688166a5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
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55 <validator type="regex" message="OrganismID[,OrganismID]">^\d+(,\d+)*$</validator> |
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0bd2688166a5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
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56 </param> |
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0bd2688166a5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
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57 </when> |
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0bd2688166a5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
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58 </conditional> |
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0bd2688166a5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
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59 </inputs> |
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0bd2688166a5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
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60 <outputs> |
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0bd2688166a5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
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61 <data format="uniprotxml" name="proteome" label="UniProtXML" /> |
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0bd2688166a5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
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62 </outputs> |
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0bd2688166a5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
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63 <tests> |
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0bd2688166a5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
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64 <test> |
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1
fc8c4bd28681
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
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65 <param name="choice" value="taxids"/> |
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0
0bd2688166a5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
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66 <param name="taxons" value="1566990"/> |
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0bd2688166a5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
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67 <output name="uniprotxml"> |
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0bd2688166a5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
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68 <assert_contents> |
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0bd2688166a5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
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69 <has_text text="</uniprot>" /> |
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0bd2688166a5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
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70 </assert_contents> |
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0bd2688166a5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
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71 </output> |
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0bd2688166a5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
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72 </test> |
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0bd2688166a5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
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73 </tests> |
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0bd2688166a5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
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74 <help> |
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75 <![CDATA[ |
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76 **UniProtXML Downloader** |
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77 |
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78 Downloads a UniProtXML file from UniProtKB |
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79 |
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80 The Morpheus proteomics search algorithm can use this format as a search database. |
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81 |
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82 Available proteomes: http://www.uniprot.org/proteomes/ |
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83 |
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84 UniProtKB help: http://www.uniprot.org/help/uniprotkb |
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85 |
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86 ]]> |
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87 </help> |
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88 <citations> |
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89 <citation type="doi">10.1093/nar/gku989</citation> |
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90 </citations> |
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91 </tool> |
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92 |