Mercurial > repos > ebi-gxa > scanpy_run_tsne

comparison scanpy-run-tsne.xml @ 5:4ed72fb8eaf8 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 400799f99ee36ad12b990b1ccabf4be16a26c003
author ebi-gxa
date Mon, 25 Nov 2019 14:39:34 -0500
parents 2e74fd7b5f45
children d85277b71596
comparison
equal deleted inserted replaced
4:45674f057a31 5:4ed72fb8eaf8
1 <?xml version="1.0" encoding="utf-8"?> 1 <?xml version="1.0" encoding="utf-8"?>
2 <tool id="scanpy_run_tsne" name="Scanpy RunTSNE" version="@TOOL_VERSION@+galaxy1"> 2 <tool id="scanpy_run_tsne" name="Scanpy RunTSNE" version="@TOOL_VERSION@+galaxy6">
3 <description>visualise cell clusters using tSNE</description> 3 <description>visualise cell clusters using tSNE</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"/>
62 <when value="false"> 62 <when value="false">
63 <param name="perplexity" argument="--perplexity" type="float" value="30" label="The perplexity is related to the number of nearest neighbours, select a value between 5 and 50"/> 63 <param name="perplexity" argument="--perplexity" type="float" value="30" label="The perplexity is related to the number of nearest neighbours, select a value between 5 and 50"/>
64 <param name="perplexity_file" argument="--perplexity" type="data" format="txt,tsv" label="The perplexity is related to the number of nearest neighbours" help="For use with the parameter iterator. Overrides the persplexity option above" optional="true"/> 64 <param name="perplexity_file" argument="--perplexity" type="data" format="txt,tsv" label="The perplexity is related to the number of nearest neighbours" help="For use with the parameter iterator. Overrides the persplexity option above" optional="true"/>
65 <param name="early_exaggeration" argument="--early-exaggeration" type="float" value="12" label="Controls the tightness within and between clusters"/> 65 <param name="early_exaggeration" argument="--early-exaggeration" type="float" value="12" label="Controls the tightness within and between clusters"/>
66 <param name="learning_rate" argument="--learning-rate" type="float" value="1000" label="Learning rate, should be between 100 and 1000"/> 66 <param name="learning_rate" argument="--learning-rate" type="float" value="1000" label="Learning rate, should be between 100 and 1000"/>
67 <param name="fast_tsne" type="boolean" checked="true" label="Use multicoreTSNE"/> 67 <param name="fast_tsne" type="boolean" checked="false" label="Use multicoreTSNE" help="Depending on the setup and version, the availability of the needed library might vary and hence fail."/>
68 <param name="n_job" argument="--n-jobs" type="integer" optional="true" label="The number of jobs"/> 68 <param name="n_job" argument="--n-jobs" type="integer" optional="true" label="The number of jobs"/>
69 <param name="n_pc" argument="--n-pcs" type="integer" optional="true" label="The number of PCs to use"/> 69 <param name="n_pc" argument="--n-pcs" type="integer" optional="true" label="The number of PCs to use"/>
70 <param name="random_seed" argument="--random-seed" type="integer" value="0" label="Seed for random number generator"/> 70 <param name="random_seed" argument="--random-seed" type="integer" value="0" label="Seed for random number generator"/>
71 </when> 71 </when>
72 </conditional> 72 </conditional>
73 73
74 </inputs> 74 </inputs>
75 75
76 <outputs> 76 <outputs>
77 <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: tSNE object"/> 77 <expand macro="output_data_obj" description="tSNE object"/>
78 <data name="output_embed" format="csv" from_work_dir="embeddings.csv" label="${tool.name} on ${on_string}: tSNE embeddings"> 78 <data name="output_embed" format="csv" from_work_dir="embeddings.csv" label="${tool.name} on ${on_string}: tSNE embeddings">
79 <filter>embeddings</filter> 79 <filter>embeddings</filter>
80 </data> 80 </data>
81 </outputs> 81 </outputs>
82 82