Mercurial > repos > earlhaminst > hcluster_sg_parser

annotate hcluster_sg_parser.xml @ 1:17aa68582a05 draft

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planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit a79c8f1799189754eae80aede6fbe5428570f36b
author earlhaminst
date Fri, 20 Jan 2017 06:13:23 -0500
parents dbc49bd1a3e9
children 0a33fd8ead70
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17aa68582a05 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit a79c8f1799189754eae80aede6fbe5428570f36b
earlhaminst
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1 <tool id="hcluster_sg_parser" name="hcluster_sg_parser" version="0.2.0">
17aa68582a05 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit a79c8f1799189754eae80aede6fbe5428570f36b
earlhaminst
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2 <description>converts hcluster_sg 3-column output into lists of IDs</description>
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3 <command>
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4 <![CDATA[
1
17aa68582a05 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit a79c8f1799189754eae80aede6fbe5428570f36b
earlhaminst
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5 python '$__tool_directory__/hcluster_sg_parser.py' '$inputFile'
17aa68582a05 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit a79c8f1799189754eae80aede6fbe5428570f36b
earlhaminst
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6 #if str($min_elems)
17aa68582a05 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit a79c8f1799189754eae80aede6fbe5428570f36b
earlhaminst
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7 -m $min_elems
17aa68582a05 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit a79c8f1799189754eae80aede6fbe5428570f36b
earlhaminst
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8 #end if
17aa68582a05 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit a79c8f1799189754eae80aede6fbe5428570f36b
earlhaminst
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9 #if str($max_elems)
17aa68582a05 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit a79c8f1799189754eae80aede6fbe5428570f36b
earlhaminst
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10 -M $max_elems
17aa68582a05 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit a79c8f1799189754eae80aede6fbe5428570f36b
earlhaminst
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11 #end if
17aa68582a05 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit a79c8f1799189754eae80aede6fbe5428570f36b
earlhaminst
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12 '$discarded'
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13 ]]>
dbc49bd1a3e9 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
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14 </command>
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earlhaminst
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15 <inputs>
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earlhaminst
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16 <param name="inputFile" type="data" format="tabular" label="hcluster output file in 3-column format" help="3-columns format: cluster_id cluster-size cluster-members" />
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17aa68582a05 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit a79c8f1799189754eae80aede6fbe5428570f36b
earlhaminst
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17 <param name="min_elems" type="integer" value="" min="0" optional="true" label="Minimum number of cluster elements" />
17aa68582a05 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit a79c8f1799189754eae80aede6fbe5428570f36b
earlhaminst
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18 <param name="max_elems" type="integer" value="" min="2" optional="true" label="Maximum number of cluster elements" />
0
dbc49bd1a3e9 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
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19 </inputs>
dbc49bd1a3e9 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
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20 <outputs>
dbc49bd1a3e9 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
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21 <collection name="ids_lists" type="list" label="${tool.name} on ${on_string}">
dbc49bd1a3e9 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
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22 <discover_datasets pattern="(?P&lt;designation&gt;.+)_output\.txt" ext="txt" />
dbc49bd1a3e9 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
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23 </collection>
1
17aa68582a05 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit a79c8f1799189754eae80aede6fbe5428570f36b
earlhaminst
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24 <data name="discarded" format="txt" label="${tool.name} on ${on_string}: discarded IDs" />
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dbc49bd1a3e9 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
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25 </outputs>
dbc49bd1a3e9 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
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26 <tests>
dbc49bd1a3e9 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
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27 <test>
dbc49bd1a3e9 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
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28 <param name="inputFile" ftype="tabular" value="hcluster_sg.tabular" />
dbc49bd1a3e9 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
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29 <output_collection name="ids_lists" type="list">
dbc49bd1a3e9 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
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30 <element name="0" file="0_output.txt" ftype="txt" />
dbc49bd1a3e9 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
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31 <element name="1" file="1_output.txt" ftype="txt" />
dbc49bd1a3e9 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
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32 <element name="2" file="2_output.txt" ftype="txt" />
dbc49bd1a3e9 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
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33 <element name="3" file="3_output.txt" ftype="txt" />
dbc49bd1a3e9 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
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34 </output_collection>
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17aa68582a05 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit a79c8f1799189754eae80aede6fbe5428570f36b
earlhaminst
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35 <output name="discarded" file="empty.txt" />
17aa68582a05 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit a79c8f1799189754eae80aede6fbe5428570f36b
earlhaminst
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36 </test>
17aa68582a05 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit a79c8f1799189754eae80aede6fbe5428570f36b
earlhaminst
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37 <test>
17aa68582a05 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit a79c8f1799189754eae80aede6fbe5428570f36b
earlhaminst
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38 <param name="inputFile" ftype="tabular" value="hcluster_sg.tabular" />
17aa68582a05 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit a79c8f1799189754eae80aede6fbe5428570f36b
earlhaminst
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39 <param name="min_elems" value="6" />
17aa68582a05 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit a79c8f1799189754eae80aede6fbe5428570f36b
earlhaminst
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40 <output_collection name="ids_lists" type="list">
17aa68582a05 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit a79c8f1799189754eae80aede6fbe5428570f36b
earlhaminst
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41 <element name="0" file="0_output.txt" ftype="txt" />
17aa68582a05 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit a79c8f1799189754eae80aede6fbe5428570f36b
earlhaminst
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42 <element name="1" file="1_output.txt" ftype="txt" />
17aa68582a05 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit a79c8f1799189754eae80aede6fbe5428570f36b
earlhaminst
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43 </output_collection>
17aa68582a05 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit a79c8f1799189754eae80aede6fbe5428570f36b
earlhaminst
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44 <output name="discarded" file="discarded.txt" />
0
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45 </test>
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46 </tests>
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47 <help>
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48 <![CDATA[
1
17aa68582a05 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit a79c8f1799189754eae80aede6fbe5428570f36b
earlhaminst
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49 A simple parser to convert the hcluster_sg 3-column output into lists of IDs, one list for each cluster.
17aa68582a05 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit a79c8f1799189754eae80aede6fbe5428570f36b
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50
17aa68582a05 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit a79c8f1799189754eae80aede6fbe5428570f36b
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51 When a minimum and/or maximum number of cluster elements are specified, the IDs contained in the filtered-out clusters are collected in the "discarded IDS" output dataset.
0
dbc49bd1a3e9 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
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52 ]]>
dbc49bd1a3e9 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
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53 </help>
dbc49bd1a3e9 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
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54 <citations>
dbc49bd1a3e9 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
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55 </citations>
dbc49bd1a3e9 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
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56 </tool>