Mercurial > repos > azomics > metacyto_preprocess
diff metacyto_preprocess.xml @ 0:bf6470882a15 draft default tip
"planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
| author | azomics |
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| date | Sun, 25 Jul 2021 10:36:03 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/metacyto_preprocess.xml Sun Jul 25 10:36:03 2021 +0000 @@ -0,0 +1,170 @@ +<tool id="metacyto_preprocess" name="Pre-process samples" version="1.0+galaxy0" profile="18.01"> + <description>for 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 a label for FCS files sets." /> + <exit_code range="12" level="fatal" description="FCS files in a same group MUST have the same set of markers." /> + <exit_code range="13" level="fatal" description="All groups needs to have different labels"/> + <exit_code range="14:" /> + </stdio> + <command><![CDATA[ + Rscript --slave --vanilla '$__tool_directory__/metacyto_preprocess.R' + '${sampling}' + 'preprocessed_fcs' + '${output_file}' + '${excluded_param}' + '${g1_name}' + '${g1_format}' + '${g1_scaling_factor}' + #for $f in $group1 + '${f}' '${f.name}' + #end for + #for $panel in $fcs_set + 'new_panel' + '${panel.gp_name}' + '${panel.gp_format}' + '${panel.gp_scaling_factor}' + #for $ff in $panel.group + '${ff}' '${ff.name}' + #end for + #end for + ]]> + </command> + <inputs> + <param name="sampling" type="integer" label="Number of events to sample FCS files to." help="0 will use all events from input files, default value is 5000." value="5000"/> + <param name="excluded_param" type="text" label="Parameters to exclude from the transformation." help="By default FSC, SSC, Time and Cell Length channels are excluded. Providing markers to exclude overrides the default setting. i.e.:FSC, SSC, CD88"/> + <param name="g1_name" type="text" label="Label for the first set of FCS files." value="group 1"/> + <param format="fcs" name="group1" type="data_collection" collection_type="list" label="FCS files Collection."/> + <param name="g1_format" type="select" label="Assay type for the first set of FCS files." help="If files are compensated already, please select CyTOF."> + <option value="FCM" selected="true">Standard Flow Cytometry data</option> + <option value="CyTOF">CyTOF data</option> + </param> + <param name="g1_scaling_factor" type="integer" min="0" max="200" value="150" label="Scaling factor b for arcsinh transform for the first set of files." help="The default value is 150 for standard FCM data. The recommended value for CyTOF data is 5. If data is transformed already, please select 0."/> + <repeat name="fcs_set" title="Set of FCS files"> + <param name="gp_name" type="text" label="Label for this set of FCS files." help="For example: group 2"/> + <param format="fcs" name="group" type="data_collection" collection_type="list" label="FCS files Collection."/> + <param name="gp_format" type="select" label="Assay type for the first set of FCS files." help="If files are compensated already, please select CyTOF."> + <option value="FCM" selected="true">Standard Flow Cytometry data</option> + <option value="CyTOF">CyTOF data</option> + </param> + <param name="gp_scaling_factor" type="integer" min="1" max="200" value="150" label="Scaling factor b for arcsinh transform for the first set of files." help="The default value is 150 for standard FCM data. The recommended value for cyTOF data is 5. If data is transformed already, please select 0."/> + </repeat> + </inputs> + <outputs> + <data format="metacyto_summary.txt" name="output_file" label="${tool.name} on ${on_string}: samples summary"/> + <collection type="list" label="${tool.name} on ${on_string}: processed samples" name="preprocessed"> + <discover_datasets directory="preprocessed_fcs" pattern="__name_and_ext__" ext="fcs" /> + </collection> + </outputs> + <tests> + <test> + <param name="sampling" value="1000"/> + <param name="excluded_param" value="FSC-A,FSC-W,FSC-H,Time,Cell_length"/> + <param name="g1_name" value="SDY376"/> + <param name="group1"> + <collection type="list"> + <element name="inputflow1" value="inputflow1.fcs"/> + <element name="inputflow2" value="inputflow2.fcs"/> + <element name="inputflow3" value="inputflow3.fcs"/> + <element name="inputflow4" value="inputflow4.fcs"/> + <element name="inputflow5" value="inputflow5.fcs"/> + <element name="inputflow6" value="inputflow6.fcs"/> + </collection> + </param> + <param name="g1_format" value="FCM"/> + <param name="g1_scaling_factor" value="150"/> + <repeat name="fcs_set"> + <param name="gp_name" value="SDY376-2"/> + <param name="group"> + <collection type="list"> + <element name="inputcytof1" value="inputcytof1.fcs"/> + <element name="inputcytof2" value="inputcytof2.fcs"/> + <element name="inputcytof3" value="inputcytof3.fcs"/> + <element name="inputcytof4" value="inputcytof4.fcs"/> + </collection> + </param> + <param name="gp_format" value="CyTOF"/> + <param name="gp_scaling_factor" value="8"/> + </repeat> + <output name="output_file"> + <assert_contents> + <has_n_lines n="11" /> + </assert_contents> + </output> + <output_collection name="preprocessed" type="list"> + <element name="SDY376" ftype="fcs"> + <assert_contents> + <has_text_matching expression="^FCS3.0" /> + </assert_contents> + </element> + <element name="SDY376-2" ftype="fcs"> + <assert_contents> + <has_text_matching expression="^FCS3.0" /> + </assert_contents> + </element> + </output_collection> + </test> + </tests> + <help><![CDATA[ + Pre-process samples + ------------------- + + This tool uses MetaCyto's preprocessing function to prepare sets of FCS files for a MetaCyto analysis. + + **Input** + This tool requires one or more sets of FCS files. + .. class:: infomark + The number provided for sub-sampling corresponds to the number of events randomly sampled from each FCS files. + **Output** + This tool generates one or more FCS files containing optionally sub-sampled data from the input FCS data sets. The FCS data can optionally be compensated and/or transformed. A summary of the operations is also generated. + .. class:: infomark + This tool uses the arcsinh transformation. If you would like to use another transformation algorithm, sets of files can be prepared independantly by using the following tools: + - Merge and downsample FCS files with FlowSOM + - Transform FCS data with optional compensation and automated gating with flowDensity. + .. class:: warningmark + The workflow to use MetaCyto in R vs. ImmPort Galaxy are slightly different - please use the following tool in FCS File Tools to harmonize FCS files before MetaCyto pre-processing: + - Edit markers or channels in FCS files + + **Example** + + *File1*: 20K events:: + + Marker1 Marker2 Marker3 ... + 34 45 12 ... + 33 65 10 ... + 87 26 76 ... + 24 56 32 ... + 95 83 53 ... + ... ... ... ... + + *File2*: 20K events:: + + Marker1 Marker2 Marker3 ... + 19 62 98 ... + 12 36 58 ... + 41 42 68 ... + 76 74 53 ... + 62 34 45 ... + ... ... ... ... + + *Output*: 5K events:: + + Marker1 Marker2 Marker3 ... + 34 45 12 ... + 87 26 76 ... + 12 36 58 ... + 62 34 45 ... + ... ... ... ... + + *Output* - Summary Table:: + + study_id antibodies filenames + group1 Marker1|Marker2|Marker3|... file1.fcs + group2 Marker1|Marker2|Marker3|... file2.fcs + ]]> + </help> +</tool>