Mercurial > repos > iuc > colibread_commet
annotate commet.xml @ 5:d03353742508 draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 8d37fef93da141323cc120b5fec737432e497dcf"
author | iuc |
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date | Thu, 06 May 2021 12:45:20 +0000 |
parents | 10e0e74c83af |
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rev | line source |
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5
d03353742508
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 8d37fef93da141323cc120b5fec737432e497dcf"
iuc
parents:
0
diff
changeset
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1 <tool id="commet" name="Commet" version="24.7.14+galaxy0" profile="@PROFILE@"> |
0
10e0e74c83af
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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2 <description>COmpare Multiple METagenomes</description> |
10e0e74c83af
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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3 <macros> |
10e0e74c83af
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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4 <import>macros.xml</import> |
10e0e74c83af
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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5 </macros> |
10e0e74c83af
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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6 <requirements> |
10e0e74c83af
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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7 <requirement type="package" version="24.7.14">commet</requirement> |
10e0e74c83af
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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8 </requirements> |
5
d03353742508
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 8d37fef93da141323cc120b5fec737432e497dcf"
iuc
parents:
0
diff
changeset
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9 <command detect_errors="exit_code"><![CDATA[ |
d03353742508
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 8d37fef93da141323cc120b5fec737432e497dcf"
iuc
parents:
0
diff
changeset
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10 #for $i, $set in enumerate($sets): |
0
10e0e74c83af
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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11 echo "set${i}: ${ ','.join(['%s' % read for read in $set.reads]) }" >> commet_input_sets.txt && |
10e0e74c83af
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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12 #end for |
10e0e74c83af
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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13 Commet.py |
10e0e74c83af
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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14 -k ${k} |
10e0e74c83af
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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15 -t ${t} |
10e0e74c83af
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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16 -l ${l} |
10e0e74c83af
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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17 -e ${e} |
5
d03353742508
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 8d37fef93da141323cc120b5fec737432e497dcf"
iuc
parents:
0
diff
changeset
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18 #if str($options_advanced.options_advanced_selector) == "advanced": |
0
10e0e74c83af
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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19 -m ${options_advanced.m} |
10e0e74c83af
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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20 -n ${options_advanced.n} |
10e0e74c83af
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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21 #end if |
10e0e74c83af
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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22 commet_input_sets.txt |
10e0e74c83af
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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23 ]]></command> |
10e0e74c83af
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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24 <inputs> |
10e0e74c83af
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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25 <repeat name="sets" title="Read sets" min="1"> |
5
d03353742508
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 8d37fef93da141323cc120b5fec737432e497dcf"
iuc
parents:
0
diff
changeset
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26 <param name="reads" type="data" multiple="true" format="fasta,fasta.gz,fastq,fastq.gz" label="Dataset" help="Accept fasta/fastq"/> |
0
10e0e74c83af
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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27 </repeat> |
10e0e74c83af
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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28 <param argument="-k" type="integer" label="Size of kmers" value="33" help="Set the length of used kmers." /> |
10e0e74c83af
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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29 <param argument="-t" type="integer" label="Mini shared kmers" value="2" help="Minimal number of shared kmers." /> |
10e0e74c83af
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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30 <param argument="-l" type="integer" label="Read mini length" value="66" help="Minimal length a read should have to be kept." /> |
10e0e74c83af
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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31 <param argument="-e" type="float" label="Mini Shannon index" value="0" min="0" max="2.32" help="Minimal Shannon index a read should have to be kept." /> |
10e0e74c83af
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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32 <conditional name="options_advanced"> |
10e0e74c83af
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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33 <param name="options_advanced_selector" type="select" label="Reads filter options" help="By default, all reads are kept with no Ns limitation"> |
10e0e74c83af
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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34 <option value="default" selected="true">default</option> |
10e0e74c83af
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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35 <option value="advanced">advanced</option> |
10e0e74c83af
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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36 </param> |
10e0e74c83af
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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37 <when value="default" /> |
10e0e74c83af
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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38 <when value="advanced"> |
10e0e74c83af
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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39 <param argument="-m" type="integer" value="-1" label="Maximum number of selected reads in sets" help="Maximum number of selected reads in sets. If a set is composed by 3 read files, and this option = 600, then the first 200 reads from each read file will be treated. (-1 = any)" /> |
10e0e74c83af
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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40 <param argument="-n" type="integer" value="-1" label="Read maxi number of Ns" help="Maximal number of Ns a read should contain to be kept. (-1 = all)" /> |
10e0e74c83af
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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41 </when> |
10e0e74c83af
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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42 </conditional> |
10e0e74c83af
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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43 <param name="normalized_outputs" label="Generate normalized files" type="boolean" checked="true"/> |
10e0e74c83af
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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44 <param name="plain_outputs" label="Generate plain files" type="boolean" checked="false"/> |
10e0e74c83af
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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45 <param name="percentage_outputs" label="Generate percentage files" type="boolean" checked="false"/> |
10e0e74c83af
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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46 </inputs> |
10e0e74c83af
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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47 <outputs> |
10e0e74c83af
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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48 <data format="csv" name="matrix_plain" from_work_dir="output_commet/matrix_plain.csv" label="Matrix plain with ${tool.name} on ${on_string}" > |
10e0e74c83af
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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49 <filter>plain_outputs</filter> |
10e0e74c83af
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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50 </data> |
10e0e74c83af
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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51 <data format="csv" name="matrix_percentage" from_work_dir="output_commet/matrix_percentage.csv" label="Matrix percentage with ${tool.name} on ${on_string}" > |
10e0e74c83af
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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52 <filter>percentage_outputs</filter> |
10e0e74c83af
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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53 </data> |
10e0e74c83af
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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54 <data format="csv" name="matrix_normalized" from_work_dir="output_commet/matrix_normalized.csv" label="Matrix normalized with ${tool.name} on ${on_string}" > |
10e0e74c83af
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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55 <filter>normalized_outputs</filter> |
10e0e74c83af
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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56 </data> |
10e0e74c83af
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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57 <data format="png" name="dendrogram_normalized" from_work_dir="output_commet/dendrogram_normalized.png" label="Dendrogram ${tool.name} on ${on_string}" /> |
10e0e74c83af
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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58 <data format="png" name="heatmap_normalized" from_work_dir="output_commet/heatmap_normalized.png" label="Heatmap normalized with ${tool.name} on ${on_string}" > |
10e0e74c83af
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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59 <filter>normalized_outputs</filter> |
10e0e74c83af
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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60 </data> |
10e0e74c83af
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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61 <data format="png" name="heatmap_percentage" from_work_dir="output_commet/heatmap_percentage.png" label="Heatmap percentage with ${tool.name} on ${on_string}" > |
10e0e74c83af
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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62 <filter>percentage_outputs</filter> |
10e0e74c83af
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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63 </data> |
10e0e74c83af
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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64 <data format="png" name="heatmap_plain" from_work_dir="output_commet/heatmap_plain.png" label="Heatmap Plain with ${tool.name} on ${on_string}" > |
10e0e74c83af
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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65 <filter>plain_outputs</filter> |
10e0e74c83af
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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66 </data> |
10e0e74c83af
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
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67 </outputs> |
10e0e74c83af
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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68 <tests> |
10e0e74c83af
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
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69 <test> |
10e0e74c83af
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
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70 <param name="input_type" value="list" /> |
10e0e74c83af
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
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71 <repeat name="sets"> |
5
d03353742508
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 8d37fef93da141323cc120b5fec737432e497dcf"
iuc
parents:
0
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72 <param name="reads" value="commet/A.fa.gz" ftype="fasta.gz" /> |
0
10e0e74c83af
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
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73 </repeat> |
10e0e74c83af
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
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74 <repeat name="sets"> |
5
d03353742508
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 8d37fef93da141323cc120b5fec737432e497dcf"
iuc
parents:
0
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75 <param name="reads" value="commet/B.fa.gz,commet/C.fa.gz" ftype="fasta.gz" /> |
0
10e0e74c83af
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
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76 </repeat> |
10e0e74c83af
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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77 <repeat name="sets"> |
5
d03353742508
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 8d37fef93da141323cc120b5fec737432e497dcf"
iuc
parents:
0
diff
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78 <param name="reads" value="commet/D.fa.gz" ftype="fasta.gz" /> |
0
10e0e74c83af
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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79 </repeat> |
10e0e74c83af
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
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80 <param name="plain_outputs" value="True"/> |
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81 <output name="dendrogram_normalized" file="commet/dendrogram.png" compare="sim_size" delta="10000"/> |
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82 <output name="matrix_plain" file="commet/matrix_plain.csv"/> |
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83 </test> |
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84 </tests> |
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85 <help><![CDATA[ |
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86 |
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87 **Description** |
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88 |
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89 COMMET (COmpare Multiple METagenomes”) provides a global similarity overview between all datasets of a large metagenomic project. |
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90 |
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91 Directly from non-assembled reads, all against all comparisons are performed through an efficient indexing strategy. Then, results are stored as bit vectors, a compressed representation of read files, that can be used to further combine read subsets by common logical operations. Finally, COMMET computes a clusterization of metagenomic datasets, which is visualized by dendrogram and heatmaps. |
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92 |
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93 |
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94 ------- |
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95 |
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96 **Web site** |
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97 |
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98 http://colibread.inria.fr/commet/ |
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99 |
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100 ]]></help> |
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101 <expand macro="citations"> |
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102 <citation type="doi">10.1186/1471-2105-13-S19-S10</citation> |
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103 </expand> |
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104 </tool> |