Mercurial > repos > earlhaminst > smart_domains

annotate smart_domains.xml @ 1:8c24cc7431aa draft default tip

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"planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 411fa9c106996050b2d2e8027e14d2068f6b14c3"
author earlhaminst
date Tue, 22 Dec 2020 04:29:12 +0000
parents a3b26189fee3
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
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1 <tool id="smart_domains" name="SMART domains" version="0.1.0">
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
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2 <description>Search domains in protein sequences using SMART</description>
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
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3 <requirements>
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
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4 <requirement type="package" version="1.6.924">perl-bioperl</requirement>
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
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5 <requirement type="package" version="2.90">perl-json</requirement>
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
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6 </requirements>
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
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7 <command detect_errors="exit_code"><![CDATA[
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
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8 perl '$__tool_directory__/smart-domain.pl'
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
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9 --inputFile='$inputFile'
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
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10 $Pfam
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
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11 $SignalP
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
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12 $Repeats
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
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13 $DISEMBL
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
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14 $Schnipsel
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
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15 $outputFormat
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
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16 ]]></command>
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
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17 <inputs>
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
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18 <param name="inputFile" type="data" format="fasta" label="Protein sequences" help="In FASTA format" />
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
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19 <param name="Pfam" type="boolean" truevalue="--includePfam" falsevalue="" label="Include Pfam domains" argument="--includePfam" />
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
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20 <param name="SignalP" type="boolean" truevalue="--includeSignalP" falsevalue="" label="Include signal peptide predictions" argument="--includeSignalP" />
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
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21 <param name="Repeats" type="boolean" truevalue="--includeRepeats" falsevalue="" label="Include internal repeat predictions" argument="--includeRepeats" />
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
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22 <param name="DISEMBL" type="boolean" truevalue="--includeDISEMBL" falsevalue="" label="Include predictions of internal protein disorder" argument="--includeDISEMBL" />
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
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23 <param name="Schnipsel" type="boolean" truevalue="--includeSchnipsel" falsevalue="" label="Include predictions of outlier homologues and homologues of known structures" argument="--includeSchnipsel" />
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
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24 <param name="outputFormat" type="select" label="Output format">
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
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25 <option value="--outputFormat=txt" selected="true">Text</option>
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
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26 <option value="--outputFormat=tabular">Tabular</option>
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
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27 <option value="--outputFormat=json">JSON</option>
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
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28 </param>
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
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29 </inputs>
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
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30 <outputs>
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
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31 <collection name="output_lists" type="list" label="${tool.name} on ${on_string}">
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
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32 <discover_datasets pattern="(?P&lt;name&gt;.+)_SMART_results\.(?P&lt;ext&gt;.+)" directory="SMART_results" />
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
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33 </collection>
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
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34 </outputs>
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
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35 <tests>
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
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36 <test>
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
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37 <param name="inputFile" ftype="fasta" value="seq.fa" />
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
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38 <param name="Pfam" value="true" />
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
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39 <param name="SignalP" value="false" />
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
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40 <param name="Repeats" value="false" />
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
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41 <param name="DISEMBL" value="false" />
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
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42 <param name="Schnipsel" value="false" />
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
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43 <param name="outputFormat" value="--outputFormat=txt" />
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
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44 <output_collection name="output_lists" type="list" count="12">
1
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45 <element name="ENSCAFP00000021307" file="ENSCAFP00000021307_SMART_results.txt" ftype="txt" compare="sim_size" delta_frac="0.1" />
8c24cc7431aa "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 411fa9c106996050b2d2e8027e14d2068f6b14c3"
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46 <element name="ENSCAFP00000021330" file="ENSCAFP00000021330_SMART_results.txt" ftype="txt" compare="sim_size" delta_frac="0.1" />
8c24cc7431aa "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 411fa9c106996050b2d2e8027e14d2068f6b14c3"
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47 <element name="ENSMUSP00000026013" file="ENSMUSP00000026013_SMART_results.txt" ftype="txt" compare="sim_size" delta_frac="0.1" />
8c24cc7431aa "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 411fa9c106996050b2d2e8027e14d2068f6b14c3"
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48 <element name="ENSMUSP00000040550" file="ENSMUSP00000040550_SMART_results.txt" ftype="txt" compare="sim_size" delta_frac="0.1" />
8c24cc7431aa "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 411fa9c106996050b2d2e8027e14d2068f6b14c3"
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49 <element name="ENSP00000340684" file="ENSP00000340684_SMART_results.txt" ftype="txt" compare="sim_size" delta_frac="0.1" />
8c24cc7431aa "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 411fa9c106996050b2d2e8027e14d2068f6b14c3"
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50 <element name="ENSP00000367309" file="ENSP00000367309_SMART_results.txt" ftype="txt" compare="sim_size" delta_frac="0.1" />
8c24cc7431aa "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 411fa9c106996050b2d2e8027e14d2068f6b14c3"
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51 <element name="ENSPTRP00000037440" file="ENSPTRP00000037440_SMART_results.txt" ftype="txt" compare="sim_size" delta_frac="0.1" />
8c24cc7431aa "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 411fa9c106996050b2d2e8027e14d2068f6b14c3"
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52 <element name="ENSPTRP00000037441" file="ENSPTRP00000037441_SMART_results.txt" ftype="txt" compare="sim_size" delta_frac="0.1" />
8c24cc7431aa "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 411fa9c106996050b2d2e8027e14d2068f6b14c3"
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53 <element name="ENSRNOP00000043466" file="ENSRNOP00000043466_SMART_results.txt" ftype="txt" compare="sim_size" delta_frac="0.1" />
8c24cc7431aa "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 411fa9c106996050b2d2e8027e14d2068f6b14c3"
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54 <element name="ENSRNOP00000063784" file="ENSRNOP00000063784_SMART_results.txt" ftype="txt" compare="sim_size" delta_frac="0.1" />
8c24cc7431aa "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 411fa9c106996050b2d2e8027e14d2068f6b14c3"
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55 <element name="ENSSSCP00000013044" file="ENSSSCP00000013044_SMART_results.txt" ftype="txt" compare="sim_size" delta_frac="0.1" />
8c24cc7431aa "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 411fa9c106996050b2d2e8027e14d2068f6b14c3"
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56 <element name="ENSSSCP00000028353" file="ENSSSCP00000028353_SMART_results.txt" ftype="txt" compare="sim_size" delta_frac="0.1" />
0
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57 </output_collection>
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58 </test>
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59 <test>
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60 <param name="inputFile" ftype="fasta" value="seq.fa" />
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61 <param name="Pfam" value="true" />
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62 <param name="SignalP" value="false" />
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63 <param name="Repeats" value="false" />
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64 <param name="DISEMBL" value="false" />
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65 <param name="Schnipsel" value="false" />
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
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66 <param name="outputFormat" value="--outputFormat=json" />
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67 <output_collection name="output_lists" type="list" count="12">
1
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68 <element name="ENSCAFP00000021307" file="ENSCAFP00000021307_SMART_results.json" ftype="json" compare="sim_size" delta_frac="0.1" />
8c24cc7431aa "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 411fa9c106996050b2d2e8027e14d2068f6b14c3"
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69 <element name="ENSCAFP00000021330" file="ENSCAFP00000021330_SMART_results.json" ftype="json" compare="sim_size" delta_frac="0.1" />
8c24cc7431aa "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 411fa9c106996050b2d2e8027e14d2068f6b14c3"
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70 <element name="ENSMUSP00000026013" file="ENSMUSP00000026013_SMART_results.json" ftype="json" compare="sim_size" delta_frac="0.1" />
8c24cc7431aa "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 411fa9c106996050b2d2e8027e14d2068f6b14c3"
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71 <element name="ENSMUSP00000040550" file="ENSMUSP00000040550_SMART_results.json" ftype="json" compare="sim_size" delta_frac="0.1" />
8c24cc7431aa "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 411fa9c106996050b2d2e8027e14d2068f6b14c3"
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72 <element name="ENSP00000340684" file="ENSP00000340684_SMART_results.json" ftype="json" compare="sim_size" delta_frac="0.1" />
8c24cc7431aa "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 411fa9c106996050b2d2e8027e14d2068f6b14c3"
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73 <element name="ENSP00000367309" file="ENSP00000367309_SMART_results.json" ftype="json" compare="sim_size" delta_frac="0.1" />
8c24cc7431aa "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 411fa9c106996050b2d2e8027e14d2068f6b14c3"
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74 <element name="ENSPTRP00000037440" file="ENSPTRP00000037440_SMART_results.json" ftype="json" compare="sim_size" delta_frac="0.1" />
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75 <element name="ENSPTRP00000037441" file="ENSPTRP00000037441_SMART_results.json" ftype="json" compare="sim_size" delta_frac="0.1" />
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76 <element name="ENSRNOP00000043466" file="ENSRNOP00000043466_SMART_results.json" ftype="json" compare="sim_size" delta_frac="0.1" />
8c24cc7431aa "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 411fa9c106996050b2d2e8027e14d2068f6b14c3"
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77 <element name="ENSRNOP00000063784" file="ENSRNOP00000063784_SMART_results.json" ftype="json" compare="sim_size" delta_frac="0.1" />
8c24cc7431aa "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 411fa9c106996050b2d2e8027e14d2068f6b14c3"
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78 <element name="ENSSSCP00000013044" file="ENSSSCP00000013044_SMART_results.json" ftype="json" compare="sim_size" delta_frac="0.1" />
8c24cc7431aa "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 411fa9c106996050b2d2e8027e14d2068f6b14c3"
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79 <element name="ENSSSCP00000028353" file="ENSSSCP00000028353_SMART_results.json" ftype="json" compare="sim_size" delta_frac="0.1" />
0
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80 </output_collection>
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81 </test>
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82 </tests>
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83 <help><![CDATA[
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
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84 A simple tool to search domains in multiple protein sequences contained in a FASTA file using the `SMART`_ web service.
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
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85
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86 Written by Ivica Letunic <ivica@letunic.com>
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87
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88 Modified by Anil Thanki <Anil.Thanki@earlham.ac.uk> to parse output in JSON and tabular format to adapt in Galaxy
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89
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90 .. _SMART: http://smart.embl.de/
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91 ]]></help>
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92 <citations>
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93 <citation type="doi">10.1073/pnas.95.11.5857</citation>
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94 <citation type="doi">10.1093/nar/gku949</citation>
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95 </citations>
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96 </tool>