Mercurial > repos > ebi-gxa > scanpy_run_paga

annotate scanpy-run-paga.xml @ 11:a1a7650c5cf2 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 62f47287c7e8449c59a1f1f454852ddc669b1b1e-dirty"
author ebi-gxa
date Mon, 07 Sep 2020 14:01:54 +0000
parents eba43c4d86b9
children 4e7d55438238
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3e53344e540d "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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1 <?xml version="1.0" encoding="utf-8"?>
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2 <tool id="scanpy_run_paga" name="Scanpy PAGA" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
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3 <description>trajectory inference</description>
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4 <macros>
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5 <import>scanpy_macros2.xml</import>
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6 </macros>
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7 <expand macro="requirements"/>
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8 <command detect_errors="exit_code"><![CDATA[
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9 ln -s '${input_obj_file}' input.h5 &&
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10 PYTHONIOENCODING=utf-8 scanpy-cli paga
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11 --groups '${groups}'
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12 #if $neighbors_key
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13 --neighbors-key '${neighbors_key}'
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14 #end if
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15 #if $key_added
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16 --key-added '${key_added}'
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17 #end if
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18 #if $use_rna_velocity
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19 --use-rna-velocity
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20 #end if
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21 @INPUT_OPTS@
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22 @OUTPUT_OPTS@
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23 ]]></command>
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25 <inputs>
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26 <expand macro="input_object_params"/>
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27 <expand macro="output_object_params"/>
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29 <param name="groups" argument="--groups" type="text" label="Name of the clustering"/>
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30 <param name="neighbors_key" argument="--neighbors-key" value="neighbors" type="text" label="Name of the slot that holds the KNN graph"/>
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31 <param name="key_added" argument="--key-added" type="text" optional="true" label="Additional suffix to the name of the slot to save the calculated trajectory"/>
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32 <param name="use_rna_velocity" type="boolean" checked="false" label="Use RNA velocity to orient edges in the abstracted graph and estimate transitions." help=" Requires that adata.uns contains a directed single-cell graph with key velocity_graph. This feature might be subject to change in the future."/>
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33 </inputs>
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35 <outputs>
4
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36 <expand macro="output_data_obj" description="PAGA object"/>
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37 </outputs>
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38
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39 <tests>
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40 <test>
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41 <param name="input_obj_file" value="find_cluster.h5"/>
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42 <param name="input_format" value="anndata"/>
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43 <param name="output_format" value="anndata"/>
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44 <param name="groups" value="louvain"/>
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45 <param name="neighbors_key" value="neighbors"/>
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46 <output name="output_h5" file="paga.h5" ftype="h5" compare="sim_size"/>
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47 </test>
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48 </tests>
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49
3e53344e540d "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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50 <help><![CDATA[
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51 ===================================================================
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52 Perform PAGA (partition-based graph abstraction) (`scanpy.tl.paga`)
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53 ===================================================================
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54
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55 Infer trajectories by mapping out the coarse-grained connectivity structures of
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56 complex manifolds of single cell KNN graphs (Wolf et al, 2019).
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57
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58 This requires to run `Scanpy FindCluster`, first.
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59
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60 It yields `paga`, connectivity graph between clusters.
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61
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62 @HELP@
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64 @VERSION_HISTORY@
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65 ]]></help>
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66 <expand macro="citations">
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67 <citation type="doi">10.1186/s13059-019-1663-x</citation>
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68 </expand>
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69 </tool>