Mercurial > repos > youyuh48 > combine_bracken_outputs

annotate combine_bracken_outputs.xml @ 0:6e90a30b214f draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/youyuh48/galaxy-tools/tree/master/tools/combine_bracken_outputs commit e6c33bbc6689e9a0a12ff3f915515d894f1b4671-dirty
author youyuh48
date Sun, 14 Jul 2024 08:45:50 +0000
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
6e90a30b214f planemo upload for repository https://github.com/youyuh48/galaxy-tools/tree/master/tools/combine_bracken_outputs commit e6c33bbc6689e9a0a12ff3f915515d894f1b4671-dirty
youyuh48
parents:
diff changeset
1 <tool id="combine_bracken_outputs" name="Combine Bracken Outputs" version="0.1.0+galaxy0" profile="19.01">
6e90a30b214f planemo upload for repository https://github.com/youyuh48/galaxy-tools/tree/master/tools/combine_bracken_outputs commit e6c33bbc6689e9a0a12ff3f915515d894f1b4671-dirty
youyuh48
parents:
diff changeset
2 <requirements>
6e90a30b214f planemo upload for repository https://github.com/youyuh48/galaxy-tools/tree/master/tools/combine_bracken_outputs commit e6c33bbc6689e9a0a12ff3f915515d894f1b4671-dirty
youyuh48
parents:
diff changeset
3 <requirement type="package" version="2.7">bracken</requirement>
6e90a30b214f planemo upload for repository https://github.com/youyuh48/galaxy-tools/tree/master/tools/combine_bracken_outputs commit e6c33bbc6689e9a0a12ff3f915515d894f1b4671-dirty
youyuh48
parents:
diff changeset
4 </requirements>
6e90a30b214f planemo upload for repository https://github.com/youyuh48/galaxy-tools/tree/master/tools/combine_bracken_outputs commit e6c33bbc6689e9a0a12ff3f915515d894f1b4671-dirty
youyuh48
parents:
diff changeset
5 <command detect_errors="exit_code"><![CDATA[
6e90a30b214f planemo upload for repository https://github.com/youyuh48/galaxy-tools/tree/master/tools/combine_bracken_outputs commit e6c33bbc6689e9a0a12ff3f915515d894f1b4671-dirty
youyuh48
parents:
diff changeset
6 #set dataset_names = []
6e90a30b214f planemo upload for repository https://github.com/youyuh48/galaxy-tools/tree/master/tools/combine_bracken_outputs commit e6c33bbc6689e9a0a12ff3f915515d894f1b4671-dirty
youyuh48
parents:
diff changeset
7 #for $report in $reports
6e90a30b214f planemo upload for repository https://github.com/youyuh48/galaxy-tools/tree/master/tools/combine_bracken_outputs commit e6c33bbc6689e9a0a12ff3f915515d894f1b4671-dirty
youyuh48
parents:
diff changeset
8 #silent dataset_names.append(str($report.element_identifier))
6e90a30b214f planemo upload for repository https://github.com/youyuh48/galaxy-tools/tree/master/tools/combine_bracken_outputs commit e6c33bbc6689e9a0a12ff3f915515d894f1b4671-dirty
youyuh48
parents:
diff changeset
9 #end for
6e90a30b214f planemo upload for repository https://github.com/youyuh48/galaxy-tools/tree/master/tools/combine_bracken_outputs commit e6c33bbc6689e9a0a12ff3f915515d894f1b4671-dirty
youyuh48
parents:
diff changeset
10
6e90a30b214f planemo upload for repository https://github.com/youyuh48/galaxy-tools/tree/master/tools/combine_bracken_outputs commit e6c33bbc6689e9a0a12ff3f915515d894f1b4671-dirty
youyuh48
parents:
diff changeset
11 combine_bracken_outputs.py
6e90a30b214f planemo upload for repository https://github.com/youyuh48/galaxy-tools/tree/master/tools/combine_bracken_outputs commit e6c33bbc6689e9a0a12ff3f915515d894f1b4671-dirty
youyuh48
parents:
diff changeset
12 --names "${",".join($dataset_names)}"
6e90a30b214f planemo upload for repository https://github.com/youyuh48/galaxy-tools/tree/master/tools/combine_bracken_outputs commit e6c33bbc6689e9a0a12ff3f915515d894f1b4671-dirty
youyuh48
parents:
diff changeset
13 --files
6e90a30b214f planemo upload for repository https://github.com/youyuh48/galaxy-tools/tree/master/tools/combine_bracken_outputs commit e6c33bbc6689e9a0a12ff3f915515d894f1b4671-dirty
youyuh48
parents:
diff changeset
14 #for $report in $reports
6e90a30b214f planemo upload for repository https://github.com/youyuh48/galaxy-tools/tree/master/tools/combine_bracken_outputs commit e6c33bbc6689e9a0a12ff3f915515d894f1b4671-dirty
youyuh48
parents:
diff changeset
15 '$report'
6e90a30b214f planemo upload for repository https://github.com/youyuh48/galaxy-tools/tree/master/tools/combine_bracken_outputs commit e6c33bbc6689e9a0a12ff3f915515d894f1b4671-dirty
youyuh48
parents:
diff changeset
16 #end for
6e90a30b214f planemo upload for repository https://github.com/youyuh48/galaxy-tools/tree/master/tools/combine_bracken_outputs commit e6c33bbc6689e9a0a12ff3f915515d894f1b4671-dirty
youyuh48
parents:
diff changeset
17 --output '$output'
6e90a30b214f planemo upload for repository https://github.com/youyuh48/galaxy-tools/tree/master/tools/combine_bracken_outputs commit e6c33bbc6689e9a0a12ff3f915515d894f1b4671-dirty
youyuh48
parents:
diff changeset
18 ]]></command>
6e90a30b214f planemo upload for repository https://github.com/youyuh48/galaxy-tools/tree/master/tools/combine_bracken_outputs commit e6c33bbc6689e9a0a12ff3f915515d894f1b4671-dirty
youyuh48
parents:
diff changeset
19 <inputs>
6e90a30b214f planemo upload for repository https://github.com/youyuh48/galaxy-tools/tree/master/tools/combine_bracken_outputs commit e6c33bbc6689e9a0a12ff3f915515d894f1b4671-dirty
youyuh48
parents:
diff changeset
20 <param name="reports" label="Bracken report files" type="data" format="tabular" min="2" multiple="True"/>
6e90a30b214f planemo upload for repository https://github.com/youyuh48/galaxy-tools/tree/master/tools/combine_bracken_outputs commit e6c33bbc6689e9a0a12ff3f915515d894f1b4671-dirty
youyuh48
parents:
diff changeset
21 </inputs>
6e90a30b214f planemo upload for repository https://github.com/youyuh48/galaxy-tools/tree/master/tools/combine_bracken_outputs commit e6c33bbc6689e9a0a12ff3f915515d894f1b4671-dirty
youyuh48
parents:
diff changeset
22 <outputs>
6e90a30b214f planemo upload for repository https://github.com/youyuh48/galaxy-tools/tree/master/tools/combine_bracken_outputs commit e6c33bbc6689e9a0a12ff3f915515d894f1b4671-dirty
youyuh48
parents:
diff changeset
23 <data name="output" format="tabular" label="Combined Bracken report file"/>
6e90a30b214f planemo upload for repository https://github.com/youyuh48/galaxy-tools/tree/master/tools/combine_bracken_outputs commit e6c33bbc6689e9a0a12ff3f915515d894f1b4671-dirty
youyuh48
parents:
diff changeset
24 </outputs>
6e90a30b214f planemo upload for repository https://github.com/youyuh48/galaxy-tools/tree/master/tools/combine_bracken_outputs commit e6c33bbc6689e9a0a12ff3f915515d894f1b4671-dirty
youyuh48
parents:
diff changeset
25 <citations>
6e90a30b214f planemo upload for repository https://github.com/youyuh48/galaxy-tools/tree/master/tools/combine_bracken_outputs commit e6c33bbc6689e9a0a12ff3f915515d894f1b4671-dirty
youyuh48
parents:
diff changeset
26 <citation type="bibtex">
6e90a30b214f planemo upload for repository https://github.com/youyuh48/galaxy-tools/tree/master/tools/combine_bracken_outputs commit e6c33bbc6689e9a0a12ff3f915515d894f1b4671-dirty
youyuh48
parents:
diff changeset
27 title = {combine_bracken_outputs},
6e90a30b214f planemo upload for repository https://github.com/youyuh48/galaxy-tools/tree/master/tools/combine_bracken_outputs commit e6c33bbc6689e9a0a12ff3f915515d894f1b4671-dirty
youyuh48
parents:
diff changeset
28 publisher = {GitHub},
6e90a30b214f planemo upload for repository https://github.com/youyuh48/galaxy-tools/tree/master/tools/combine_bracken_outputs commit e6c33bbc6689e9a0a12ff3f915515d894f1b4671-dirty
youyuh48
parents:
diff changeset
29 journal = {GitHub repository},
6e90a30b214f planemo upload for repository https://github.com/youyuh48/galaxy-tools/tree/master/tools/combine_bracken_outputs commit e6c33bbc6689e9a0a12ff3f915515d894f1b4671-dirty
youyuh48
parents:
diff changeset
30 url = {https://github.com/jenniferlu717/Bracken}
6e90a30b214f planemo upload for repository https://github.com/youyuh48/galaxy-tools/tree/master/tools/combine_bracken_outputs commit e6c33bbc6689e9a0a12ff3f915515d894f1b4671-dirty
youyuh48
parents:
diff changeset
31 </citation>
6e90a30b214f planemo upload for repository https://github.com/youyuh48/galaxy-tools/tree/master/tools/combine_bracken_outputs commit e6c33bbc6689e9a0a12ff3f915515d894f1b4671-dirty
youyuh48
parents:
diff changeset
32 </citations>
6e90a30b214f planemo upload for repository https://github.com/youyuh48/galaxy-tools/tree/master/tools/combine_bracken_outputs commit e6c33bbc6689e9a0a12ff3f915515d894f1b4671-dirty
youyuh48
parents:
diff changeset
33 </tool>