Mercurial > repos > azomics > metacyto_search_cl

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"planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
author azomics
date Wed, 28 Jul 2021 22:02:38 +0000
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94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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1 <tool id="metacyto_search_clr" name="Guided identification of clusters" version="1.0+galaxy0" profile="18.01">
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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2 <description>using MetaCyto</description>
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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3 <requirements>
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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4 <requirement type="package" version="1.4.0">bioconductor-metacyto</requirement>
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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5 </requirements>
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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6 <stdio>
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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7 <exit_code range="1:9" />
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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8 <exit_code range="10" level="fatal" description="Please provide valid input FCS files." />
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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9 <exit_code range="11" level="fatal" description="Please provide FCS files pre-processed for MetaCyto." />
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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10 <exit_code range="12" level="fatal" description="Pre-processing summary doesn't match the set of FCS files." />
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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11 <exit_code range="13" level="fatal" description="The pre-processing summary is in the wrong format." />
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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12 <exit_code range="14" level="fatal" description="Please provide a cluster definition" />
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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13 <exit_code range="15:" />
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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14 </stdio>
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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15 <command><![CDATA[
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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16 Rscript --slave --vanilla '$__tool_directory__/metacyto_search_clr.R' '${summary}' 'fcs_stats' '${first_def}' '${unused}' '${cluster_list}'
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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17 #for $r in $cl_df
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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18 '${r.cluster_def}'
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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19 #end for
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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20 'FCS_FILES'
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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21 #for $f in $group
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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22 '${f}' '${f.name}'
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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23 #end for
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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24 ]]>
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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25 </command>
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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26 <inputs>
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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27 <param format="metacyto_summary.txt" name="summary" type="data" label="MetaCyto preprocessing summary"/>
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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28 <param format="fcs" name="group" type="data_collection" collection_type="list" label="FCS files Collection pre-processed for MetaCyto"/>
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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29 <param name="first_def" type="text" label="Cluster definition" help="i.e.:CD3+,CD4-,CD8+,CCR7+"/>
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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30 <repeat name="cl_df" title="Cluster">
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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31 <param name="cluster_def" type="text" label="Additional cluster definition" help="i.e.:CD3+,CD4-,CD8+,CCR7+"/>
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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32 </repeat>
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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33 </inputs>
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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34 <outputs>
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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35 <data format="tabular" name="unused" label="List of clusters not found in all files from ${group.name}"/>
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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36 <data format="metacyto_clr.txt" name="cluster_list" label="List of clusters from guided clustering analysis of ${group.name}"/>
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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37 <collection type="list" label="Guided cluster identification analysis in ${group.name}" name="output">
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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38 <discover_datasets pattern="(?P&lt;name&gt;.*)" directory="fcs_stats" format="metacyto_stats.txt" />
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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39 </collection>
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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40 </outputs>
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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41 <tests>
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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42 <test>
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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43 <param name="summary" value="preprocess.metacyto_summary.txt"/>
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44 <param name="group">
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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45 <collection type="list">
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46 <element name="Group1" value="Group1.fcs"/>
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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47 <element name="Group2" value="Group2.fcs"/>
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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48 </collection>
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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49 </param>
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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50 <param name="first_def" value="CD3+,CD4-,CD8+" />
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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51 <repeat name="cl_df">
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52 <param name="cluster_def" value="CD8+,CCR7+" />
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53 </repeat>
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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54 <output name="unused" >
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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55 <assert_contents>
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56 <has_n_lines n="2"/>
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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57 </assert_contents>
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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58 </output>
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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59 <output_collection name="output">
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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60 <element name="Group2_cluster_stats.txt">
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61 <assert_contents>
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62 <has_n_lines n="9"/>
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63 </assert_contents>
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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64 </element>
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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65 </output_collection>
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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66 </test>
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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67 </tests>
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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68 <help><![CDATA[
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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69 This tool uses MetaCyto to search for clusters of cells corresponding to provided gate definitions
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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70 --------------------------------------------------------------------------------------------------
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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71
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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72 **Input files**
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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73
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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74 This tool requires the pre-processing summary generated for MetaCyto as well as the pre-processed FCS files.
94ac403d134a "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
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75
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76 *Cluster definitions*
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77
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78 Please provide gate definitions as comma-separated lists of marker names, for instance "CD3+, CD4+, CD25+, Foxp3+".
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79
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80 **Output**
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81
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82 This tool generates a list of provided clusters definitions, as well as a table of the MFI for each marker in each cluster in each file, and proportion of each cluster in each file. A list of unused cluster definitions, if any, is also generated.
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83
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84 **Example**
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85
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86 *Input* - Pre-Processing Summary Table
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87
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88 ======== =========================== =========
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89 study_id antibodies filenames
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90 ======== =========================== =========
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91 group1 Marker1|Marker2|Marker3|... file1.fcs
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92 group2 Marker1|Marker2|Marker3|... file2.fcs
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93 ... ... ...
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94 ======== =========================== =========
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95
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96
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97 *Output* - Clustering Summary Tables
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98
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99 ========== ================ ========== ========================== ================ ======= ======= === ========
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100 group_name fcs_files cluster_id label fcs_names Marker1 Marker2 ... fraction
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101 ========== ================ ========== ========================== ================ ======= ======= === ========
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102 group1 file1_group1.fcs cluster1 Marker1+|Marker2+|Marker3+ file1_group1.fcs 1.9815 0.2024 ... 0.373
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103 group1 file2_group1.fcs cluster1 Marker1+|Marker2+|Marker3+ file2_group1.fcs 2.3739 0.3377 ... 0.26
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104 ... ... ... ... ... ... ... ... ...
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105 ========== ================ ========== ========================== ================ ======= ======= === ========
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106 ]]>
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107 </help>
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108 </tool>