Mercurial > repos > azomics > metacyto_search_cl
diff metacyto_search_clr.xml @ 0:94ac403d134a draft default tip
"planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
author | azomics |
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date | Wed, 28 Jul 2021 22:02:38 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/metacyto_search_clr.xml Wed Jul 28 22:02:38 2021 +0000 @@ -0,0 +1,108 @@ +<tool id="metacyto_search_clr" name="Guided identification of clusters" version="1.0+galaxy0" profile="18.01"> + <description>using MetaCyto</description> + <requirements> + <requirement type="package" version="1.4.0">bioconductor-metacyto</requirement> + </requirements> + <stdio> + <exit_code range="1:9" /> + <exit_code range="10" level="fatal" description="Please provide valid input FCS files." /> + <exit_code range="11" level="fatal" description="Please provide FCS files pre-processed for MetaCyto." /> + <exit_code range="12" level="fatal" description="Pre-processing summary doesn't match the set of FCS files." /> + <exit_code range="13" level="fatal" description="The pre-processing summary is in the wrong format." /> + <exit_code range="14" level="fatal" description="Please provide a cluster definition" /> + <exit_code range="15:" /> + </stdio> + <command><![CDATA[ + Rscript --slave --vanilla '$__tool_directory__/metacyto_search_clr.R' '${summary}' 'fcs_stats' '${first_def}' '${unused}' '${cluster_list}' + #for $r in $cl_df + '${r.cluster_def}' + #end for + 'FCS_FILES' + #for $f in $group + '${f}' '${f.name}' + #end for + ]]> + </command> + <inputs> + <param format="metacyto_summary.txt" name="summary" type="data" label="MetaCyto preprocessing summary"/> + <param format="fcs" name="group" type="data_collection" collection_type="list" label="FCS files Collection pre-processed for MetaCyto"/> + <param name="first_def" type="text" label="Cluster definition" help="i.e.:CD3+,CD4-,CD8+,CCR7+"/> + <repeat name="cl_df" title="Cluster"> + <param name="cluster_def" type="text" label="Additional cluster definition" help="i.e.:CD3+,CD4-,CD8+,CCR7+"/> + </repeat> + </inputs> + <outputs> + <data format="tabular" name="unused" label="List of clusters not found in all files from ${group.name}"/> + <data format="metacyto_clr.txt" name="cluster_list" label="List of clusters from guided clustering analysis of ${group.name}"/> + <collection type="list" label="Guided cluster identification analysis in ${group.name}" name="output"> + <discover_datasets pattern="(?P<name>.*)" directory="fcs_stats" format="metacyto_stats.txt" /> + </collection> + </outputs> + <tests> + <test> + <param name="summary" value="preprocess.metacyto_summary.txt"/> + <param name="group"> + <collection type="list"> + <element name="Group1" value="Group1.fcs"/> + <element name="Group2" value="Group2.fcs"/> + </collection> + </param> + <param name="first_def" value="CD3+,CD4-,CD8+" /> + <repeat name="cl_df"> + <param name="cluster_def" value="CD8+,CCR7+" /> + </repeat> + <output name="unused" > + <assert_contents> + <has_n_lines n="2"/> + </assert_contents> + </output> + <output_collection name="output"> + <element name="Group2_cluster_stats.txt"> + <assert_contents> + <has_n_lines n="9"/> + </assert_contents> + </element> + </output_collection> + </test> + </tests> + <help><![CDATA[ +This tool uses MetaCyto to search for clusters of cells corresponding to provided gate definitions +-------------------------------------------------------------------------------------------------- + +**Input files** + +This tool requires the pre-processing summary generated for MetaCyto as well as the pre-processed FCS files. + +*Cluster definitions* + +Please provide gate definitions as comma-separated lists of marker names, for instance "CD3+, CD4+, CD25+, Foxp3+". + +**Output** + +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. + +**Example** + +*Input* - Pre-Processing Summary Table + +======== =========================== ========= +study_id antibodies filenames +======== =========================== ========= +group1 Marker1|Marker2|Marker3|... file1.fcs +group2 Marker1|Marker2|Marker3|... file2.fcs +... ... ... +======== =========================== ========= + + +*Output* - Clustering Summary Tables + +========== ================ ========== ========================== ================ ======= ======= === ======== +group_name fcs_files cluster_id label fcs_names Marker1 Marker2 ... fraction +========== ================ ========== ========================== ================ ======= ======= === ======== +group1 file1_group1.fcs cluster1 Marker1+|Marker2+|Marker3+ file1_group1.fcs 1.9815 0.2024 ... 0.373 +group1 file2_group1.fcs cluster1 Marker1+|Marker2+|Marker3+ file2_group1.fcs 2.3739 0.3377 ... 0.26 + ... ... ... ... ... ... ... ... ... +========== ================ ========== ========================== ================ ======= ======= === ======== + ]]> + </help> +</tool>