| Previous changeset 0:885db50f1bc1 (2019-11-19) |
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Commit message:
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 7034937deaaf56b2e6f585bb28234a86a5b5fa2e |
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modified:
sccaf_macros.xml sccaf_regress_out.xml |
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| diff -r 885db50f1bc1 -r 5ef0610e9f50 sccaf_macros.xml --- a/sccaf_macros.xml Tue Nov 19 13:06:04 2019 -0500 +++ b/sccaf_macros.xml Mon Nov 25 06:28:23 2019 -0500 |
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| @@ -4,7 +4,7 @@ <requirement type="package" version="@TOOL_VERSION@">sccaf</requirement> </requirements> </xml> - <token name="@TOOL_VERSION@">0.0.8</token> + <token name="@TOOL_VERSION@">0.0.9</token> <token name="@SCCAF_INTRO@"> SCCAF explained =============== @@ -67,18 +67,22 @@ </citations> </xml> <xml name="input_object_params"> - <param name="input_obj_file" argument="--input-object-file" type="data" format="h5" label="Input object in AnnData hdf5 format" help="Normally the result of Scanpy (or equivalent), which already has both a visualisation (either tSNE, UMAP or PCA - needed) and clustering (ideally) pre-computed."/> - <param name="input_format" argument="--input-format" type="select" label="Format of input object"> - <option value="anndata" selected="true">AnnData format hdf5</option> - <option value="loom">Loom format hdf5, current support is incomplete</option> - </param> + <param name="input_obj_file" argument="--input-object-file" type="data" format="h5,h5ad" label="Input object in AnnData hdf5 format" help="Normally the result of Scanpy (or equivalent), which already has both a visualisation (either tSNE, UMAP or PCA - needed) and clustering (ideally) pre-computed."/> </xml> <xml name="output_object_params"> <param name="output_format" argument="--output-format" type="select" label="Format of output object"> - <option value="anndata" selected="true">AnnData format hdf5</option> - <option value="loom">Loom format hdf5, current support is defective</option> + <option value="anndata_h5ad" selected="true">AnnData format hdf5</option> + <option value="anndata">AnnData format (h5 for older versions)</option> </param> </xml> + <xml name="output_data_obj" token_description="operation"> + <data name="output_h5ad" format="h5ad" from_work_dir="output.h5" label="${tool.name} on ${on_string}: @DESCRIPTION@ AnnData"> + <filter>output_format == 'anndata_h5ad'</filter> + </data> + <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: @DESCRIPTION@ AnnData"> + <filter>output_format == 'anndata'</filter> + </data> + </xml> <xml name="output_plot_params"> <param name="color_by" argument="--color-by" type="text" value="n_genes" label="Color by attributes, comma separated strings"/> <param name="groups" argument="--groups" type="text" optional="ture" label="Restrict plotting to named groups, comma separated strings"/> |
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| diff -r 885db50f1bc1 -r 5ef0610e9f50 sccaf_regress_out.xml --- a/sccaf_regress_out.xml Tue Nov 19 13:06:04 2019 -0500 +++ b/sccaf_regress_out.xml Mon Nov 25 06:28:23 2019 -0500 |
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| @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="utf-8"?> -<tool id="sccaf_regress_out" name="SCCAF mulitple regress out" version="@TOOL_VERSION@+galaxy0"> +<tool id="sccaf_regress_out" name="SCCAF mulitple regress out" version="@TOOL_VERSION@+galaxy1"> <description>with multiple categorical keys on an AnnData object.</description> <macros> <import>sccaf_macros.xml</import> @@ -11,10 +11,11 @@ ]]></command> <inputs> <param name="input_obj_file" argument="input-object-file" type="data" format="h5" label="Input object in hdf5 AnnData format"/> + <expand macro="output_object_params"/> <param name="keys_to_regress" label="Keys to regress" help="Comma separated keys for regressing out; they need to exist in the observations part of the AnnData object." type="text"/> </inputs> <outputs> - <data name="output" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: regressesed out on ${keys_to_regress}"/> + <expand macro="output_data_obj" description="regressed out on ${keys_to_regress}"/> </outputs> <tests> @@ -22,7 +23,7 @@ <param name="input_obj_file" value="find_cluster.h5"/> <param name="input_format" value="anndata"/> <param name="color_by" value="louvain"/> - <output name="output" file="output.h5" ftype="h5" compare="sim_size"/> + <output name="output_h5ad" file="output.h5" ftype="h5" compare="sim_size"/> </test> </tests> |