Mercurial > repos > ppericard > mixomics_blocksplsda

annotate matCor_addVar.xml @ 6:bc28839b17fb 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/bilille/galaxy-mixomics-blocksplsda commit f2b28f1a77491a26f8ac753b3623400d8485470a
author ppericard
date Tue, 10 Mar 2020 06:51:08 -0400
parents b0ab97ffc2a1
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
4
b0ab97ffc2a1 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 0bf5c0745f406f2eca9c708a062c975b1f7ea386
ppericard
parents: 3
diff changeset
1 <tool id="matCor_addVar" name="matCor_addVar" version="0.3.0" profile="16.04" workflow_compatible="true">
3
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2
4
b0ab97ffc2a1 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 0bf5c0745f406f2eca9c708a062c975b1f7ea386
ppericard
parents: 3
diff changeset
3 <description>computes all the correlations needed to plot a correlation circle and determines which correlation circles can be superimposed</description>
b0ab97ffc2a1 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 0bf5c0745f406f2eca9c708a062c975b1f7ea386
ppericard
parents: 3
diff changeset
4
3
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
5 <requirements>
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
6 <requirement type="package" version="6.8">bioconductor-mixomics</requirement>
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
7 <requirement type="package" version="2.0">r-argparse</requirement>
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
8 </requirements>
4
b0ab97ffc2a1 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 0bf5c0745f406f2eca9c708a062c975b1f7ea386
ppericard
parents: 3
diff changeset
9
3
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
10 <stdio>
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
11 <!-- <exit_code range="1:" level="fatal" /> -->
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
12 </stdio>
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
13
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
14 <command detect_errors="aggressive">
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
15 <![CDATA[
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
16 Rscript
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
17 ${__tool_directory__}/matCor_addVar_wrapper.R
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
18 --input_rdata ${input_rdata}
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
19 --cutoff_comp ${cutoff_comp}
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
20 --mat_block_Y_file ${mat_block_Y}
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
21 --output_rdata ${output_rdata}
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
22 --output_blocks_comb ${output_blocks_comb}
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
23 ]]>
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
24 </command>
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
25
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
26 <inputs>
4
b0ab97ffc2a1 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 0bf5c0745f406f2eca9c708a062c975b1f7ea386
ppericard
parents: 3
diff changeset
27 <param name="input_rdata" type="data" format="rdata"
b0ab97ffc2a1 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 0bf5c0745f406f2eca9c708a062c975b1f7ea386
ppericard
parents: 3
diff changeset
28 label="Input RData file from block.SPLSDA"
b0ab97ffc2a1 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 0bf5c0745f406f2eca9c708a062c975b1f7ea386
ppericard
parents: 3
diff changeset
29 help="This is the RData output file from the block.splsda function." />
b0ab97ffc2a1 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 0bf5c0745f406f2eca9c708a062c975b1f7ea386
ppericard
parents: 3
diff changeset
30 <param name="cutoff_comp" type="float" value="0.8" min="0" max="1"
b0ab97ffc2a1 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 0bf5c0745f406f2eca9c708a062c975b1f7ea386
ppericard
parents: 3
diff changeset
31 label="Cutoff comp"
b0ab97ffc2a1 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 0bf5c0745f406f2eca9c708a062c975b1f7ea386
ppericard
parents: 3
diff changeset
32 help="[cutoff_comp] Two correlation circles will be superimposed if the correlation of their first and second axis is greater than cutoff_comp in absolute value." />
b0ab97ffc2a1 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 0bf5c0745f406f2eca9c708a062c975b1f7ea386
ppericard
parents: 3
diff changeset
33 <param name="mat_block_Y" type="data" format="tabular"
b0ab97ffc2a1 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 0bf5c0745f406f2eca9c708a062c975b1f7ea386
ppericard
parents: 3
diff changeset
34 label="Matrix Block Y"
b0ab97ffc2a1 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 0bf5c0745f406f2eca9c708a062c975b1f7ea386
ppericard
parents: 3
diff changeset
35 help="Matrix Block Y in tabular format. This table contains the name of the samples in the first column. The other columns correspond to phenotypes. For each of these other columns, a column determines which sample is associated with this phenotype (value equals to 1) or not (value equals to 0). The name of the samples in Matrix Block Y (transposed), in the sample metadata (transposed) and for all datasets have to be in the same order" />
3
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
36 </inputs>
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
37
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
38 <outputs>
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
39 <data name="output_rdata" format="rdata" label="${tool.name}_output.rdata" />
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
40 <data name="output_blocks_comb" format="tabular" label="${tool.name}_blocks_comb.tsv" />
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
41 </outputs>
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
42
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
43 <tests>
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
44 </tests>
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
45
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
46 <help>
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
47 </help>
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
48
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
49 </tool>