Mercurial > repos > galaxyp > uniprotxml_downloader
annotate uniprotxml_downloader.xml @ 5:265c35540faa draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit ba0d41c2dc0dbc0a0d3d200f51e67c6598c7e4e9
| author | galaxyp |
|---|---|
| date | Fri, 04 Nov 2022 15:08:37 +0000 |
| parents | 12692567c7f9 |
| children | a371252a2cf6 |
| rev | line source |
|---|---|
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5
265c35540faa
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit ba0d41c2dc0dbc0a0d3d200f51e67c6598c7e4e9
galaxyp
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changeset
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1 <tool id="uniprotxml_downloader" name="UniProt" version="2.3.0" profile="21.01"> |
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2
e1abc9a35c64
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
galaxyp
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changeset
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2 <description>download proteome as XML or fasta</description> |
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5
265c35540faa
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit ba0d41c2dc0dbc0a0d3d200f51e67c6598c7e4e9
galaxyp
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3 <macros> |
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265c35540faa
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit ba0d41c2dc0dbc0a0d3d200f51e67c6598c7e4e9
galaxyp
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4 <import>macros.xml</import> |
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265c35540faa
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit ba0d41c2dc0dbc0a0d3d200f51e67c6598c7e4e9
galaxyp
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5 </macros> |
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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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6 <requirements> |
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4
12692567c7f9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 62afd9de6db50f4314e49d9f24881b6d3778a0a5"
galaxyp
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7 <requirement type="package" version="2.25.1">requests</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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8 </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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9 <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
parents:
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changeset
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10 <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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11 </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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12 <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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13 <![CDATA[ |
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12692567c7f9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 62afd9de6db50f4314e49d9f24881b6d3778a0a5"
galaxyp
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14 python '$__tool_directory__/uniprotxml_downloader.py' |
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e1abc9a35c64
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
galaxyp
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15 #if $taxid.input_choice == 'common': |
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4
12692567c7f9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 62afd9de6db50f4314e49d9f24881b6d3778a0a5"
galaxyp
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16 --taxon $taxid.organism |
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5
265c35540faa
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit ba0d41c2dc0dbc0a0d3d200f51e67c6598c7e4e9
galaxyp
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17 --field taxonomy_id |
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4
12692567c7f9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 62afd9de6db50f4314e49d9f24881b6d3778a0a5"
galaxyp
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changeset
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18 #if $taxid.reviewed: |
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12692567c7f9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 62afd9de6db50f4314e49d9f24881b6d3778a0a5"
galaxyp
parents:
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changeset
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19 --reviewed=$taxid.reviewed |
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12692567c7f9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 62afd9de6db50f4314e49d9f24881b6d3778a0a5"
galaxyp
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20 #end if |
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2
e1abc9a35c64
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
galaxyp
parents:
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21 #elif $taxid.input_choice == 'taxids': |
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5
265c35540faa
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit ba0d41c2dc0dbc0a0d3d200f51e67c6598c7e4e9
galaxyp
parents:
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diff
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22 --field $taxid.field |
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4
12692567c7f9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 62afd9de6db50f4314e49d9f24881b6d3778a0a5"
galaxyp
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23 #for $id in $taxid.taxons.split(','): |
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12692567c7f9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 62afd9de6db50f4314e49d9f24881b6d3778a0a5"
galaxyp
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24 -t '$id' |
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12692567c7f9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 62afd9de6db50f4314e49d9f24881b6d3778a0a5"
galaxyp
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25 #end for |
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2
e1abc9a35c64
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
galaxyp
parents:
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changeset
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26 #elif $taxid.input_choice == 'history': |
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5
265c35540faa
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit ba0d41c2dc0dbc0a0d3d200f51e67c6598c7e4e9
galaxyp
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diff
changeset
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27 --field $taxid.field |
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4
12692567c7f9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 62afd9de6db50f4314e49d9f24881b6d3778a0a5"
galaxyp
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28 --input='${taxid.taxon_file}' |
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12692567c7f9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 62afd9de6db50f4314e49d9f24881b6d3778a0a5"
galaxyp
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29 --column=#echo int(str($taxid.column)) - 1# |
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2
e1abc9a35c64
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
galaxyp
parents:
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30 #end if |
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4
12692567c7f9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 62afd9de6db50f4314e49d9f24881b6d3778a0a5"
galaxyp
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31 --format $format |
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12692567c7f9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 62afd9de6db50f4314e49d9f24881b6d3778a0a5"
galaxyp
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32 --output '${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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33 ]]> |
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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 </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:
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changeset
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35 <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
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36 <conditional name="taxid"> |
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2
e1abc9a35c64
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
galaxyp
parents:
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37 <param name="input_choice" type="select" label="Select"> |
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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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38 <option value="common">A Common Organism</option> |
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4
12692567c7f9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 62afd9de6db50f4314e49d9f24881b6d3778a0a5"
galaxyp
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39 <option value="taxids">A manually entered list of Taxon IDs or names</option> |
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12692567c7f9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 62afd9de6db50f4314e49d9f24881b6d3778a0a5"
galaxyp
parents:
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40 <option value="history">A history dataset with a column containing Taxon IDs or names</option> |
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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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41 </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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42 <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:
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43 <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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44 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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45 <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:
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46 <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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47 <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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48 </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:
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49 </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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50 <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
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51 <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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52 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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53 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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54 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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55 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
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56 ]]> |
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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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57 </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
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58 <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
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59 <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
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60 </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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61 </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
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62 <when value="taxids"> |
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2
e1abc9a35c64
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
galaxyp
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63 <param name="taxons" type="text" label="NCBI Taxon IDs or names" |
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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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64 help="Enter one or more Organsim IDs (separated by commas) from http://www.uniprot.org/proteomes/"> |
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2
e1abc9a35c64
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
galaxyp
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65 <validator type="regex" message="OrganismID[,OrganismID]">^\w+( \w+)*(,\w+( \w+)*)*$</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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66 </param> |
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5
265c35540faa
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit ba0d41c2dc0dbc0a0d3d200f51e67c6598c7e4e9
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67 <expand macro="query_field"/> |
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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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68 </when> |
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2
e1abc9a35c64
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
galaxyp
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69 <when value="history"> |
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4
12692567c7f9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 62afd9de6db50f4314e49d9f24881b6d3778a0a5"
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70 <param name="taxon_file" type="data" format="tabular,txt" label="Dataset (tab separated) with Taxon ID/Name column"/> |
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12692567c7f9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 62afd9de6db50f4314e49d9f24881b6d3778a0a5"
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71 <param name="column" type="data_column" data_ref="taxon_file" label="Column with Taxon ID/name"/> |
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5
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72 <expand macro="query_field"/> |
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2
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
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73 </when> |
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0
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
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74 </conditional> |
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2
e1abc9a35c64
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
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75 <param name="format" type="select" label="uniprot output format"> |
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e1abc9a35c64
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
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76 <option value="xml">xml</option> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
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77 <option value="fasta">fasta</option> |
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e1abc9a35c64
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
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78 </param> |
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0
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
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79 </inputs> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
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80 <outputs> |
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2
e1abc9a35c64
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
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81 <data format="uniprotxml" name="proteome" label="UniProt.${format}"> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
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82 <change_format> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
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83 <when input="format" value="fasta" format="fasta" /> |
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e1abc9a35c64
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
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84 </change_format> |
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e1abc9a35c64
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
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85 </data> |
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0
0bd2688166a5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
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86 </outputs> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
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87 <tests> |
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88 <test> |
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2
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89 <param name="input_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
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90 <param name="taxons" value="1566990"/> |
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2
e1abc9a35c64
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
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91 <param name="format" value="xml"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
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92 <output name="proteome"> |
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0
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93 <assert_contents> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
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94 <has_text text="</uniprot>" /> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
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95 </assert_contents> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
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96 </output> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
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97 </test> |
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2
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
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98 <test> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
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99 <param name="input_choice" value="taxids"/> |
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5
265c35540faa
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit ba0d41c2dc0dbc0a0d3d200f51e67c6598c7e4e9
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100 <param name="taxons" value="765963,512562"/> |
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265c35540faa
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit ba0d41c2dc0dbc0a0d3d200f51e67c6598c7e4e9
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101 <param name="field" value="taxonomy_id"/> |
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265c35540faa
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit ba0d41c2dc0dbc0a0d3d200f51e67c6598c7e4e9
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102 <param name="format" value="fasta"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit ba0d41c2dc0dbc0a0d3d200f51e67c6598c7e4e9
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103 <output name="proteome"> |
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265c35540faa
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit ba0d41c2dc0dbc0a0d3d200f51e67c6598c7e4e9
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104 <assert_contents> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit ba0d41c2dc0dbc0a0d3d200f51e67c6598c7e4e9
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105 <has_text text="Shi470" /> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit ba0d41c2dc0dbc0a0d3d200f51e67c6598c7e4e9
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106 <has_text text="PeCan4" /> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit ba0d41c2dc0dbc0a0d3d200f51e67c6598c7e4e9
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107 </assert_contents> |
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265c35540faa
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit ba0d41c2dc0dbc0a0d3d200f51e67c6598c7e4e9
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108 </output> |
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109 </test> |
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110 <test> |
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265c35540faa
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit ba0d41c2dc0dbc0a0d3d200f51e67c6598c7e4e9
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111 <param name="input_choice" value="taxids"/> |
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2
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112 <param name="taxons" value="Shi470,PeCan4"/> |
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5
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit ba0d41c2dc0dbc0a0d3d200f51e67c6598c7e4e9
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113 <param name="field" value="taxonomy_name"/> |
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2
e1abc9a35c64
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
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114 <param name="format" value="fasta"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
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115 <output name="proteome"> |
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e1abc9a35c64
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
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116 <assert_contents> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
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117 <has_text text="Shi470" /> |
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e1abc9a35c64
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
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118 <has_text text="PeCan4" /> |
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e1abc9a35c64
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
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119 </assert_contents> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
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120 </output> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
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121 </test> |
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e1abc9a35c64
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
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122 <test> |
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e1abc9a35c64
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
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123 <param name="input_choice" value="history"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
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124 <param name="taxon_file" value="Helicobacter_strains.tsv" ftype="tabular"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
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125 <param name="column" value="1"/> |
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5
265c35540faa
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit ba0d41c2dc0dbc0a0d3d200f51e67c6598c7e4e9
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126 <param name="field" value="taxonomy_name"/> |
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2
e1abc9a35c64
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
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127 <param name="format" value="fasta"/> |
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e1abc9a35c64
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
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128 <output name="proteome"> |
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e1abc9a35c64
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
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129 <assert_contents> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
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130 <has_text text="Shi470" /> |
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e1abc9a35c64
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
galaxyp
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131 <has_text text="PeCan4" /> |
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e1abc9a35c64
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
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132 </assert_contents> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
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133 </output> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
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134 </test> |
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4
12692567c7f9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 62afd9de6db50f4314e49d9f24881b6d3778a0a5"
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135 <test> |
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12692567c7f9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 62afd9de6db50f4314e49d9f24881b6d3778a0a5"
galaxyp
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136 <param name="input_choice" value="history"/> |
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12692567c7f9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 62afd9de6db50f4314e49d9f24881b6d3778a0a5"
galaxyp
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137 <param name="taxon_file" value="Helicobacter_strains_ids.tsv" ftype="tabular"/> |
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12692567c7f9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 62afd9de6db50f4314e49d9f24881b6d3778a0a5"
galaxyp
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138 <param name="column" value="2"/> |
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5
265c35540faa
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit ba0d41c2dc0dbc0a0d3d200f51e67c6598c7e4e9
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139 <param name="field" value="taxonomy_id"/> |
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4
12692567c7f9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 62afd9de6db50f4314e49d9f24881b6d3778a0a5"
galaxyp
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140 <param name="format" value="fasta"/> |
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12692567c7f9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 62afd9de6db50f4314e49d9f24881b6d3778a0a5"
galaxyp
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141 <output name="proteome"> |
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12692567c7f9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 62afd9de6db50f4314e49d9f24881b6d3778a0a5"
galaxyp
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142 <assert_contents> |
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12692567c7f9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 62afd9de6db50f4314e49d9f24881b6d3778a0a5"
galaxyp
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143 <has_text text="Shi470" /> |
|
12692567c7f9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 62afd9de6db50f4314e49d9f24881b6d3778a0a5"
galaxyp
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144 <has_text text="PeCan4" /> |
|
12692567c7f9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 62afd9de6db50f4314e49d9f24881b6d3778a0a5"
galaxyp
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145 </assert_contents> |
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146 </output> |
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147 </test> |
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148 </tests> |
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149 <help> |
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150 <![CDATA[ |
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151 **UniProt Downloader** |
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152 |
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153 Downloads either a UniProtXML file or a fasta file from UniProtKB |
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154 |
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155 The Morpheus proteomics search algorithm can use the UniProtXML format as a search database. |
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156 |
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157 Available proteomes: http://www.uniprot.org/proteomes/ |
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158 |
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159 Available taxon names: http://www.uniprot.org/taxonomy/ |
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160 |
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161 Example taxon: http://www.uniprot.org/taxonomy/512562 |
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162 |
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163 Taxon IDs or names can be entered as text or read from a column in a tabular dataset from your history. |
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164 |
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165 Example IDs and names releated to the Bacteria Helicobacter pylori (strain Shi470) :: |
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166 |
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167 |
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168 - 512562 |
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169 - Shi470 |
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170 - Helicobacter pylori |
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171 - Helicobacter |
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172 - Helicobacteraceae |
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173 |
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174 |
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175 UniProtKB help: http://www.uniprot.org/help/uniprotkb |
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176 |
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177 ]]> |
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178 </help> |
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179 <citations> |
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180 <citation type="doi">10.1093/nar/gku989</citation> |
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181 </citations> |
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182 </tool> |
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183 |