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annotate sccaf_asses.xml @ 0:95670267a5b6 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/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
author ebi-gxa
date Mon, 14 Oct 2019 08:10:33 -0400
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95670267a5b6 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
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1 <?xml version="1.0" encoding="utf-8"?>
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2 <tool id="sccaf_asses" name="SCCAF Assesment" version="@TOOL_VERSION@+galaxy0">
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3 <description>runs an assesment of an SCCAF optimisation result or an existing clustering.</description>
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4 <macros>
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5 <import>sccaf_macros.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 &&
95670267a5b6 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
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11 sccaf-assess -i input.h5 --iterations $iterations --cores \${GALAXY_SLOTS:-1}
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12 -o sccaf_assess.txt
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13 #if $rounds_file
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14 --slot-for-existing-clustering \$( cat $rounds_file )
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15 #else
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16 --slot-for-existing-clustering $existing_slot
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17 #end if
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19
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20 ]]></command>
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21
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22 <inputs>
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23 <expand macro="input_object_params"/>
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24
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25 <conditional name="slot_source">
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26 <param type="select" name="source" label="Choose the source of the slot for existing clustering" help="either a round file or an explicit name of a round.">
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27 <option value="explicit" selected="True">Input the desired round directly</option>
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28 <option value="file">Input the desired round through a file</option>
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29 </param>
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30 <when value="explicit">
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31 <param type="text" value="" name="existing_slot" label="Specific round to asses" help="Write the slot of the AnnData object that you want assessed."/>
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32 </when>
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33 <when value="file">
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34 <param name="rounds_file" argument="--slot-for-existing-clustering" type="data" format="txt,tsv" label="A file containing a single round to asses in the AnnData file." help="For use with sccaf_distribute_assesment" optional="true"/>
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35 </when>
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36 </conditional>
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37 <param type="integer" value="5" name="iterations" label="Iterations for assesment" help="The number of times that the assesment is internally repeated to achieve a result."/>
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38
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39 </inputs>
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40
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41 <outputs>
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42 <data name="output_table" format="txt" from_work_dir="sccaf_assess.txt" label="${tool.name} on ${on_string} assesment accuracy and cross validation."/>
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43 <data name="output_png" format="png" from_work_dir="roc-curve.png" label="${tool.name} on ${on_string} ROC-Curve">
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44 <filter>iterations == 1</filter>
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45 </data>
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46 </outputs>
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47
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48 <tests>
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49 <test>
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50 <param name="input_obj_file" value="find_cluster.h5"/>
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51 <param name="use_tsv" value="true"/>
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52 <param name="input_tsv" value="find_cluster.tsv"/>
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53 <output name="output_png" file="run_sccaf.png" ftype="png"/>
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54 </test>
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55 </tests>
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56
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57 <help><![CDATA[
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58 @SCCAF_INTRO@
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59
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60 SCCAF Assesment
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61 ===============
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62
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63 This module is used to independently asses either SCCAF Optimisation rounds
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64 results or just any clustering contained in an AnnData object that contains also
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65 UMAP embeddings (necessary for the plots shown). The main purpose of this
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66 independent assesment module is to distribute assesment runs after an optimisation.
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67
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68
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69 ]]></help>
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70 <!-- <expand macro="citations"/> -->
95670267a5b6 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 68be7a6fdb93e8b59e80e5f16e7fecdaa16f288c
ebi-gxa
parents:
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71 </tool>