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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
author iuc
date Tue, 31 Aug 2021 08:38:20 +0000
parents 3d76702452e1
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a365150d73c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
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1 <tool id="heinz" name="Identify optimal scoring subnetwork" version="1.0">
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2 <description>using Heinz</description>
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e520fbedf79b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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3 <xrefs>
e520fbedf79b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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4 <xref type="bio.tools">heinz</xref>
e520fbedf79b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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5 </xrefs>
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6 <requirements>
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7 <requirement type="package" version="2.0">heinz</requirement>
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8 </requirements>
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9 <command detect_errors="aggressive"><![CDATA[
1
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10 heinz -m \${GALAXY_SLOTS:-2} -n '$score' -e '$edge' > '$subnetwork'
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11 ]]></command>
a365150d73c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
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12 <inputs>
1
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13 <param name="score" type="data" format="txt" label="File containing Heinz scores"
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14 help="The file should contain two columns: the node identifier (e.g. gene) and the corresponding Heinz score" />
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15 <param name="edge" type="data" format="txt" label="Edge file"
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16 help="In this file, two nodes define one edge, one edge per line" />
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17 </inputs>
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18 <outputs>
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19 <data name="subnetwork" format="txt" label="${tool.name} on ${on_string}: Optimal subgraph" />
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20 </outputs>
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21 <tests>
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22 <test>
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23 <param name="score" value="NodesPCST.txt" />
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24 <param name="edge" value="EdgesPCST.txt" />
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25 <output name="subnetwork">
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26 <assert_contents>
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27 <has_text text='label="a\n5\n0\n0"' />
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28 <has_text text='label="b\n-4\n0\n1",shape=box' />
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29 <has_text text="Total weight: 36" />
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30 <has_text text="0 -- 1" />
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31 <has_text text="1 -- 3" />
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32 <has_text text="5 -- 7" />
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33 </assert_contents>
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34 </output>
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35 </test>
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36 </tests>
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37 <help><![CDATA[
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38 **Note**: You are currently using a version of Heinz based on IBM CPLEX Community version,
a365150d73c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
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39 which is limiting the capacity of Heinz in handling big networks. For an unlimited version of Heinz,
a365150d73c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
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40 you need to get a license of IBM CPLEX and compile Heinz from scratch from here https://github.com/ls-cwi/heinz.
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41 We are currently looking for an alternative to IBM CPLEX in Heinz to make an unlimited version of Heinz available
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42 to the public as soon as possible.
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43
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44 Score file --- the output file of the tool "Calculate Heinz scores": two columns delimited
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45 by a tab without headers, the first column is node identifier (e.g., genes, KEGG ORTHOLOGY (KO));
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46 the second, Heinz score.
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47
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48 ========= ===================
1
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49 BRCA2 -6.991782933819368
0
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50 --------- -------------------
1
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51 BRCA1 -5.206139799106934
0
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52 --------- -------------------
1
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53 AACS -0.9299868303078357
0
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54 --------- -------------------
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55 ABCC11 -5.845009850430119
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56 ========= ===================
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57
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58 Edge file: the background network Heinz uses in the form of a list of edges; each line is made up of
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59 two node identifiers (e.g., genes, KEGG ORTHOLOGY (KO)) delimited by a tab. In practice, we could
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60 prepare this file using different pathway databases, such as Reactome, STRING and KEGG. Which database
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61 to choose depends on the question to solve.
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62
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63 ========= =========
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64 ACTR1B ACVR2B
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65 --------- ---------
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66 ZSWIM9 FOXP3
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67 --------- ---------
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68 LGALS4 PRKX
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69 --------- ---------
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70 NPTX1 CIAO1
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71 ========= =========
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72 ]]></help>
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73 <citations>
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74 <citation type="doi">10.1093/bioinformatics/btn161</citation>
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75 </citations>
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76 </tool>