| Previous changeset 0:02b1fe7aed76 (2023-10-02) Next changeset 2:0e70b2dfe4be (2023-12-01) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit 576069ce2296ef58daa8a4e03c993d5900608c4c |
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modified:
baredsc_1d.xml macros.xml |
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| diff -r 02b1fe7aed76 -r 4fff5a293013 baredsc_1d.xml --- a/baredsc_1d.xml Mon Oct 02 13:24:52 2023 +0000 +++ b/baredsc_1d.xml Mon Oct 16 14:01:08 2023 +0000 |
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| @@ -58,27 +58,27 @@ </section> </inputs> <outputs> - <data format="npz" name="output" label="${tool.name} on $getVar('input_counts.input', 'input_counts.inputAnnData') for ${geneColName}: Numpy archive" from_work_dir="output.npz"/> - <data format="txt" name="neff" label="${tool.name} on $getVar('input_counts.input', 'input_counts.inputAnnData') for ${geneColName}: Neff" from_work_dir="output/baredSC_neff.txt"/> - <collection type="list" name="qc_plots" label="${tool.name} on $getVar('input_counts.input', 'input_counts.inputAnnData') for ${geneColName}: QC plots"> + <data format="npz" name="output" label="${tool.name} on $getVar('input_counts.input', $getVar('input_counts.inputAnnData', 'shouldNeverHappen')).element_identifier for ${geneColName}: Numpy archive" from_work_dir="output.npz"/> + <data format="txt" name="neff" label="${tool.name} on $getVar('input_counts.input', $getVar('input_counts.inputAnnData', 'shouldNeverHappen')).element_identifier for ${geneColName}: Neff" from_work_dir="output/baredSC_neff.txt"/> + <collection type="list" name="qc_plots" label="${tool.name} on $getVar('input_counts.input', $getVar('input_counts.inputAnnData', 'shouldNeverHappen')).element_identifier for ${geneColName}: QC plots"> <discover_datasets pattern="baredSC_(?P<identifier_0>\S+)\.(?P<ext>.*)" directory="QC"/> </collection> - <data format="tabular" name="pdf" label="${tool.name} on $getVar('input_counts.input', 'input_counts.inputAnnData') for ${geneColName}: PDF with error bar" from_work_dir="output/baredSC_pdf.txt"> + <data format="tabular" name="pdf" label="${tool.name} on $getVar('input_counts.input', $getVar('input_counts.inputAnnData', 'shouldNeverHappen')).element_identifier for ${geneColName}: PDF with error bar" from_work_dir="output/baredSC_pdf.txt"> <actions> <action name="column_names" type="metadata" default="x,low,mean,high,median" /> </actions> </data> - <data format="png" name="plot" label="${tool.name} on $getVar('input_counts.input', 'input_counts.inputAnnData') for ${geneColName}: plot" from_work_dir="baredSC"> + <data format="png" name="plot" label="${tool.name} on $getVar('input_counts.input', $getVar('input_counts.inputAnnData', 'shouldNeverHappen')).element_identifier for ${geneColName}: plot" from_work_dir="baredSC"> <change_format> <when input="plots.image_file_format" value="png" format="png" /> <when input="plots.image_file_format" value="svg" format="svg" /> <when input="plots.image_file_format" value="pdf" format="pdf" /> </change_format> </data> - <collection type="list" name="other_outputs" label="${tool.name} on $getVar('input_counts.input', 'input_counts.inputAnnData') for ${geneColName}: plots and txt"> + <collection type="list" name="other_outputs" label="${tool.name} on $getVar('input_counts.input', $getVar('input_counts.inputAnnData', 'shouldNeverHappen')).element_identifier for ${geneColName}: plots and txt"> <discover_datasets pattern="baredSC_(?P<identifier_0>\S+)\.(?P<ext>.*)"/> </collection> - <data format="txt" name="logevidence" label="${tool.name} on $getVar('input_counts.input', 'input_counts.inputAnnData') for ${geneColName}: Log evidence" from_work_dir="logevidence.txt"/> + <data format="txt" name="logevidence" label="${tool.name} on $getVar('input_counts.input', $getVar('input_counts.inputAnnData', 'shouldNeverHappen')).element_identifier for ${geneColName}: Log evidence" from_work_dir="logevidence.txt"/> </outputs> <tests> <!-- First test --> |
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| diff -r 02b1fe7aed76 -r 4fff5a293013 macros.xml --- a/macros.xml Mon Oct 02 13:24:52 2023 +0000 +++ b/macros.xml Mon Oct 16 14:01:08 2023 +0000 |
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| @@ -1,5 +1,5 @@ <macros> - <token name="@TOOL_VERSION@">1.1.1</token> + <token name="@TOOL_VERSION@">1.1.2</token> <token name="@VERSION_SUFFIX@">0</token> <xml name="requirements"> <requirements> @@ -49,7 +49,7 @@ <param argument="--input" type="data" format="tabular" label="Input table (with header)" help="Expected format is one line per cell, columns with raw counts and one column 'nCount_RNA' with the total number of UMI per cell (optionally other meta data to filter)" /> </when> <when value="anndata"> - <param argument="--inputAnnData" type="data" format="anndata" label="AnnData containing raw counts" /> + <param argument="--inputAnnData" type="data" format="h5ad" label="AnnData containing raw counts" /> </when> </conditional> </xml> |