Mercurial > repos > ebi-gxa > scanpy_run_pca

comparison scanpy-run-pca.xml @ 16:988edd5fa902 draft

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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit b03a24b2e459a00c79221b160d9187902a4098d0-dirty"
author ebi-gxa
date Wed, 25 Nov 2020 16:22:51 +0000
parents 3e7ede8e1c94
children da13741428bf
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15:7ee4417b24cc 16:988edd5fa902
1 <?xml version="1.0" encoding="utf-8"?> 1 <?xml version="1.0" encoding="utf-8"?>
2 <tool id="scanpy_run_pca" name="Scanpy RunPCA" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> 2 <tool id="scanpy_run_pca" name="Scanpy RunPCA" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
3 <description>for dimensionality reduction</description> 3 <description>for dimensionality reduction</description>
4 <macros> 4 <macros>
5 <import>scanpy_macros2.xml</import> 5 <import>scanpy_macros2.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements"/> 7 <expand macro="requirements"/>
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9 ln -s '${input_obj_file}' input.h5 && 9 ln -s '${input_obj_file}' input.h5 &&
10 PYTHONIOENCODING=utf-8 scanpy-run-pca 10 PYTHONIOENCODING=utf-8 scanpy-run-pca
11 #if $n_pcs
11 --n-comps '${n_pcs}' 12 --n-comps '${n_pcs}'
13 #end if
12 #if $run_mode.chunked 14 #if $run_mode.chunked
13 --chunked 15 --chunked
14 --chunk-size '${run_mode.chunk_size}' 16 --chunk-size '${run_mode.chunk_size}'
15 #else 17 #else
16 ${run_mode.zero_center} 18 ${run_mode.zero_center}
29 ]]></command> 31 ]]></command>
30 32
31 <inputs> 33 <inputs>
32 <expand macro="input_object_params"/> 34 <expand macro="input_object_params"/>
33 <expand macro="output_object_params"/> 35 <expand macro="output_object_params"/>
34 <param name="n_pcs" argument="--n-comps" type="integer" min="2" value="50" label="Number of PCs to produce"/> 36 <param name="n_pcs" argument="--n-comps" type="integer" optional="true" min="2" value="" label="Number of PCs to produce"/>
35 <conditional name="run_mode"> 37 <conditional name="run_mode">
36 <param name="chunked" argument="--chunked" type="boolean" checked="false" label="Perform incremental PCA by chunks"/> 38 <param name="chunked" argument="--chunked" type="boolean" checked="false" label="Perform incremental PCA by chunks"/>
37 <when value="true"> 39 <when value="true">
38 <param name="chunk_size" argument="--chunk-size" type="integer" value="0" label="Chunk size"/> 40 <param name="chunk_size" argument="--chunk-size" type="integer" value="0" label="Chunk size"/>
39 </when> 41 </when>