annotate scmap_select_features.xml @ 8:e5aaa5bea06a draft

"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit a1ad1ddd9b8e4db5bb82c3accae8311e0e488b19"
author ebi-gxa
date Fri, 27 Nov 2020 13:44:55 +0000
parents 5972aea41e0e
children 91f29745bda6
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
7
5972aea41e0e "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 824146613fdab1de5bf430e01422417a720fe3f2"
ebi-gxa
parents: 4
diff changeset
1 <tool id="scmap_select_features" name="Scmap select features" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
0
22b605f49f5f "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
2 <description>finds the most informative features (genes/transcripts) for projection.</description>
22b605f49f5f "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
3 <macros>
22b605f49f5f "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
4 <import>scmap_macros.xml</import>
22b605f49f5f "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
5 </macros>
22b605f49f5f "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
6 <expand macro="requirements" />
22b605f49f5f "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
7 <command detect_errors="exit_code"><![CDATA[
1
953c7ff4069e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit b9472e45f909300389b426955f4f563b8428ed07
ebi-gxa
parents: 0
diff changeset
8 scmap-preprocess-sce.R --input-object "${input_single_cell_experiment}" --output-sce-object "${input_single_cell_experiment}.preprocessed" && scmap-select-features.R --input-object-file "${input_single_cell_experiment}.preprocessed" --n-features '$n_features' --output-object-file '$output_single_cell_experiment' --output-plot-file '$plot'
0
22b605f49f5f "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
9 ]]></command>
22b605f49f5f "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
10 <inputs>
22b605f49f5f "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
11 <param type="data" name="input_single_cell_experiment" label="SingleCellExperiment object" format="rdata" help="File with serialized SingleCellExperiment object" />
22b605f49f5f "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
12 <param name="n_features" type="integer" label="Number of features" value="500" help="Number of features to be selected" />
22b605f49f5f "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
13 </inputs>
22b605f49f5f "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
14 <outputs>
22b605f49f5f "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
15 <data name="output_single_cell_experiment" format="rdata" />
22b605f49f5f "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
16 <data name="plot" format="png" />
22b605f49f5f "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
17 </outputs>
22b605f49f5f "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
18 <tests>
22b605f49f5f "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
19 <test>
22b605f49f5f "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
20 <param name="input_single_cell_experiment" value="test_sce.rds" ftype="rdata"/>
2
3e22b96ba4fb "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 542b6e6848acedbbedb6fa2d4b44c8d476597cdd"
ebi-gxa
parents: 1
diff changeset
21 <output name="output_single_cell_experiment" file="select_features.rds" compare="sim_size"/>
8
e5aaa5bea06a "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit a1ad1ddd9b8e4db5bb82c3accae8311e0e488b19"
ebi-gxa
parents: 7
diff changeset
22 <output name="plot" file="select_features.png" compare="sim_size" delta="1000000" />
0
22b605f49f5f "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
23 </test>
22b605f49f5f "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
24 </tests>
22b605f49f5f "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
25 <help><![CDATA[
22b605f49f5f "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
26 @HELP@
22b605f49f5f "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
27
22b605f49f5f "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
28 @VERSION_HISTORY@
22b605f49f5f "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
29 ]]></help>
22b605f49f5f "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
30 <expand macro="citations" />
22b605f49f5f "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
ebi-gxa
parents:
diff changeset
31 </tool>