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Feature/scanpy_mtx_compression #259

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Feature/scanpy_mtx_compression #259

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d3b475a
Add param mtx_compression
irisdianauy Mar 3, 2022
131c4fa
Change option label
irisdianauy Mar 3, 2022
ce09327
Add conditionals to export_mtx input params and outputs
irisdianauy Mar 4, 2022
c83aabb
Change output conditionals to filters
irisdianauy Mar 7, 2022
85534a6
Use outputs collections
irisdianauy Mar 7, 2022
92c255f
Add test to check compression options
irisdianauy Mar 7, 2022
6469139
Edit test 2
irisdianauy Mar 7, 2022
2bca602
Correct tags
irisdianauy Mar 7, 2022
407e265
Correct when values
irisdianauy Mar 7, 2022
c1f8c57
Correct test 2 export-mtx param value
irisdianauy Mar 7, 2022
051d6e9
Add test with mtx export and compression option
irisdianauy Mar 7, 2022
05fec85
Add missing when block in one of the conditionals
irisdianauy Mar 7, 2022
2a7b8da
Add matrix compression options to relevant token
irisdianauy Mar 8, 2022
9bc721f
Remove compression option tests
irisdianauy Mar 8, 2022
cc48718
Edit export token
irisdianauy Mar 8, 2022
eee2d25
Add test assertions
irisdianauy Mar 8, 2022
41c0201
Revert to original save_raw test value
irisdianauy Mar 8, 2022
8dc0b50
Edit required scanpy-scripts version
irisdianauy Mar 8, 2022
a77395f
Change test output size assertion
irisdianauy Mar 8, 2022
adf807f
Require specific scanpy-scripts version
irisdianauy Mar 9, 2022
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107 changes: 103 additions & 4 deletions tools/tertiary-analysis/scanpy/scanpy_macros2.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -155,18 +155,117 @@ EMBL-EBI https://www.ebi.ac.uk/ and Teichmann Lab at Wellcome Sanger Institute.
</xml>

<xml name="export_mtx_params">
<param name="export_mtx" argument="--export-mtx" type="boolean" truevalue="--export-mtx ./" falsevalue="" checked="false" label="Save to 10x mtx format" help="If enabled, it will generate in addition to the main output in Loom or AnnData an export in 10x format."/>
<conditional name="export_mtx_inputs">
<param name="export_mtx" argument="--export-mtx" type="boolean" truevalue="--export-mtx ./" falsevalue="" checked="false" label="Save to 10x mtx format" help="If enabled, it will generate in addition to the main output in Loom or AnnData an export in 10x format."/>
<when value="true">
<param name="mtx_compression" argument="--mtx-compression" type="select" value="None" label="" help="Compression type for MTX output.">
<option value="None">No compression</option>
<option value="zip">zip</option>
<option value="gzip">gzip</option>
<option value="bz2">bz2</option>
<option value="zstd">zstd</option>
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if zst is not supported in Galaxy then we should remove it for now.

</param>
</when>
</conditional>
</xml>

<xml name="export_mtx_outputs">
<data name="matrix_10x" format="txt" from_work_dir="matrix.mtx" label="${tool.name} on ${on_string}: 10x matrix">
<data name="matrix_10x" label="${tool.name} on ${on_string}: 10x matrix">
<filter>export_mtx</filter>
<actions>
<conditional name="mtx_compression">
<when value="None">
<action type="format">
<!-- I want to update data "matrix_10x" with format="txt" from_work_dir="matrix.mtx" -->
</action>
</when>
<when value="zip">
<action type="format">
<!-- I want to update data "matrix_10x" with format="zip" from_work_dir="matrix.mtx.zip" -->
</action>
</when>
<when value="gzip">
<action type="format">
<!-- I want to update data "matrix_10x" with format="gzip" from_work_dir="matrix.mtx.gz" -->
</action>
</when>
<when value="bz2">
<action type="format">
<!-- I want to update data "matrix_10x" with format="bz2" from_work_dir="matrix.mtx.bz2" -->
</action>
</when>
<when value="zstd">
<action type="format">
<!-- I want to update data "matrix_10x" with format="zstd" from_work_dir="matrix.mtx.zst" -->
</action>
</when>
</conditional>
</actions>
</data>
<data name="genes_10x" format="tsv" from_work_dir="genes.tsv" label="${tool.name} on ${on_string}: 10x genes">
<data name="genes_10x" label="${tool.name} on ${on_string}: 10x genes">
<filter>export_mtx</filter>
<actions>
<conditional name="mtx_compression">
<when value="None">
<action type="format">
<!-- I want to update data "genes_10x" with format="tsv" from_work_dir="genes.tsv" -->
</action>
</when>
<when value="zip">
<action type="format">
<!-- I want to update data "genes_10x" with format="zip" from_work_dir="genes.tsv.zip" -->
</action>
</when>
<when value="gzip">
<action type="format">
<!-- I want to update data "genes_10x" with format="gzip" from_work_dir="genes.tsv.gz" -->
</action>
</when>
<when value="bz2">
<action type="format">
<!-- I want to update data "genes_10x" with format="bz2" from_work_dir="genes.tsv.bz2" -->
</action>
</when>
<when value="zstd">
<action type="format">
<!-- I want to update data "genes_10x" with format="zst" from_work_dir="genes.tsv.zst" -->
</action>
</when>
</conditional>
</actions>
</data>
<data name="barcodes_10x" format="tsv" from_work_dir="barcodes.tsv" label="${tool.name} on ${on_string}: 10x barcodes">
<data name="barcodes_10x" label="${tool.name} on ${on_string}: 10x barcodes">
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I would have multiple outputs, each attached to a potential value of the format.

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Done in 85534a6

<filter>export_mtx</filter>
<actions>
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It might be that these actions require a higher profile than 18.01?

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Thank you, I'll check this.

<conditional name="mtx_compression">
<when value="None">
<action type="format">
<!-- I want to update data "barcodes_10x" with format="tsv" from_work_dir="barcodes.tsv -->
</action>
</when>
<when value="zip">
<action type="format">
<!-- I want to update data "barcodes_10x" with format="zip" from_work_dir="barcodes.tsv.zip" -->
</action>
</when>
<when value="gzip">
<action type="format">
<!-- I want to update data "barcodes_10x" with format="gzip" from_work_dir="barcodes.tsv.gz" -->
</action>
</when>
<when value="bz2">
<action type="format">
<!-- I want to update data "barcodes_10x" with format="bz2" from_work_dir="barcodes.tsv.bz2" -->
</action>
</when>
<when value="zstd">
<action type="format">
<!-- I want to update data "barcodes_10x" with format="zstd" from_work_dir="barcodes.tsv.zst" -->
</action>
</when>
</conditional>
</actions>
</data>
</xml>

</macros>