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update cellranger.xml #93

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Jul 21, 2023
Merged

update cellranger.xml #93

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22 changes: 14 additions & 8 deletions tools/cellranger/cellranger.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -31,17 +31,23 @@
--sample=$collection_identifier
--transcriptome=$tool_cond.reference_source.ref_file.fields.path
--localcores=\${GALAXY_SLOTS:-2}
--localmem=\${GALAXY_MEMORY_GB:-8} &&
2>&1
--localmem=\${GALAXY_MEMORY_GB:-8}
&& gunzip output_directory/outs/filtered_feature_bc_matrix/matrix.mtx.gz
&& gunzip output_directory/outs/filtered_feature_bc_matrix/features.tsv.gz
&& gunzip output_directory/outs/filtered_feature_bc_matrix/barcodes.tsv.gz
&& 2>&1
#elif str( $tool_cond.reference_source.reference_source_selector ) == "history"
tar -xzvf '${tool_cond.reference_source.own_ref_file}' &&
cellranger count --id=output_directory
--fastqs=$fastq_directory
--sample=$collection_identifier
--transcriptome=reference_directory
--localcores=\${GALAXY_SLOTS:-2}
--localmem=\${GALAXY_MEMORY_GB:-8} &&
2>&1
--localmem=\${GALAXY_MEMORY_GB:-8}
&& gunzip output_directory/outs/filtered_feature_bc_matrix/matrix.mtx.gz
&& gunzip output_directory/outs/filtered_feature_bc_matrix/features.tsv.gz
&& gunzip output_directory/outs/filtered_feature_bc_matrix/barcodes.tsv.gz
&& 2>&1
#end if
#elif str($tool_cond.tool) == "mkref"
cellranger mkref --genome=reference_directory
Expand Down Expand Up @@ -104,18 +110,18 @@
<data format="binary" name="cloupe" label="Cloupe file from ${tool.name} on ${on_string}" from_work_dir="output_directory/outs/cloupe.cloupe">
<filter>tool_cond['tool'] == 'count'</filter>
</data>
<data format="mtx.gz" name="matrix" label="Matrix file from ${tool.name} on ${on_string}" from_work_dir="output_directory/outs/filtered_feature_bc_matrix/matrix.mtx.gz">
<data format="mtx" name="matrix" label="Matrix file from ${tool.name} on ${on_string}" from_work_dir="output_directory/outs/filtered_feature_bc_matrix/matrix.mtx">
<filter>tool_cond['tool'] == 'count'</filter>
</data>
<data format="tabular.gz" name="feature" label="Feature file from ${tool.name} on ${on_string}" from_work_dir="output_directory/outs/filtered_feature_bc_matrix/features.tsv.gz">
<data format="tabular" name="feature" label="Feature file from ${tool.name} on ${on_string}" from_work_dir="output_directory/outs/filtered_feature_bc_matrix/features.tsv">
<filter>tool_cond['tool'] == 'count'</filter>
</data>
<data format="tabular.gz" name="barcode" label="Barcode file from ${tool.name} on ${on_string}" from_work_dir="output_directory/outs/filtered_feature_bc_matrix/barcodes.tsv.gz">
<data format="tabular" name="barcode" label="Barcode file from ${tool.name} on ${on_string}" from_work_dir="output_directory/outs/filtered_feature_bc_matrix/barcodes.tsv">
<filter>tool_cond['tool'] == 'count'</filter>
</data>
<collection name="output" type="list" label="CellRanger on ${on_string}: count">
<discover_datasets pattern="(?P&lt;designation&gt;.+)\.(?P&lt;ext&gt;h5)" directory="output_directory/outs" format="h5" visible="false" />
<discover_datasets pattern="(?P&lt;designation&gt;.+)\.bam" directory="output_directory/outs" format="bam" visible="false" />
<discover_datasets pattern="(?P&lt;designation&gt;.+)\.(?P&lt;ext&gt;bam)" directory="output_directory/outs" format="bam" visible="false" />
<filter>tool_cond['tool'] == 'count'</filter>
</collection>

Expand Down
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