| Previous changeset 2:48d9421bf176 (2024-07-05) Next changeset 4:fef8f61cb34c (2024-07-23) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984 |
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modified:
macros.xml preprocessing.xml |
| b |
| diff -r 48d9421bf176 -r 4ecdea4cbea1 macros.xml --- a/macros.xml Fri Jul 05 11:06:01 2024 +0000 +++ b/macros.xml Wed Jul 17 05:54:44 2024 +0000 |
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| @@ -1,16 +1,16 @@ <macros> - <token name="@TOOL_VERSION@">2.5.3</token> - <token name="@VERSION_SUFFIX@">2</token> + <token name="@TOOL_VERSION@">2.6.4</token> + <token name="@VERSION_SUFFIX@">0</token> <token name="@PROFILE@">23.0</token> <xml name="requirements"> <requirement type="package" version="@TOOL_VERSION@">snapatac2</requirement> - <requirement type="package" version="5.18.0">plotly</requirement> + <requirement type="package" version="5.22.0">plotly</requirement> <requirement type="package" version="0.2.1">python-kaleido</requirement> - <requirement type="package" version="0.19.19">polars</requirement> - <requirement type="package" version="14.0.1">pyarrow</requirement> - <requirement type="package" version="0.11.3">python-igraph</requirement> - <requirement type="package" version="0.8.33">hdbscan</requirement> - <requirement type="package" version="0.0.9">harmonypy</requirement> + <requirement type="package" version="1.1.0">polars</requirement> + <requirement type="package" version="16.1.0">pyarrow</requirement> + <requirement type="package" version="0.11.6">python-igraph</requirement> + <requirement type="package" version="0.8.37">hdbscan</requirement> + <requirement type="package" version="0.0.10">harmonypy</requirement> <requirement type="package" version="1.7.4">scanorama</requirement> <requirement type="package" version="3.0.1">macs3</requirement> <requirement type="package" version="0.70.16">multiprocess</requirement> @@ -158,10 +158,10 @@ <has_text_matching expression="height = 450"/> </xml> <xml name="param_counting_strategy"> - <param argument="counting_strategy" type="select" label="he strategy to compute feature counts"> - <option value="fragment">fragment</option> - <option value="insertion" selected="true">insertion</option> - <option value="paired-insertion">paired-insertion</option> + <param argument="counting_strategy" type="select" label="The strategy to compute feature counts"> + <option value="fragment">"fragment": based on the number of fragments that overlap with a region of interest</option> + <option value="insertion" selected="true">"insertion": based on the number of insertions that overlap with a region of interest</option> + <option value="paired-insertion">"paired-insertion": similar to "insertion", but it only counts the insertions once if the pair of insertions of a fragment are both within the same region of interest</option> </param> </xml> |
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| diff -r 48d9421bf176 -r 4ecdea4cbea1 preprocessing.xml --- a/preprocessing.xml Fri Jul 05 11:06:01 2024 +0000 +++ b/preprocessing.xml Wed Jul 17 05:54:44 2024 +0000 |
| [ |
| @@ -85,8 +85,7 @@ #if $method.max_frag_size max_frag_size = $method.max_frag_size, #end if - ##counting_strategy = '$method.counting_strategy', - count_frag_as_reads = $method.count_frag_as_reads, + counting_strategy = '$method.counting_strategy', n_jobs = int(os.getenv("GALAXY_SLOTS", 4)) ) @@ -107,8 +106,7 @@ #if $method.max_frag_size max_frag_size = $method.max_frag_size, #end if - ##counting_strategy = '$method.counting_strategy' - count_frag_as_reads = $method.count_frag_as_reads + counting_strategy = '$method.counting_strategy' ) #else if $method.method == 'pp.filter_cells' @@ -285,8 +283,7 @@ <expand macro="sanitize_query"/> </param> <expand macro="min_max_frag_size"/> - <!--expand macro="param_counting_strategy"/--> - <param argument="count_frag_as_reads" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Whether to count fragments as reads"/> + <expand macro="param_counting_strategy"/> </when> <when value="pp.make_gene_matrix"> <expand macro="inputs_anndata"/> @@ -302,8 +299,7 @@ <param argument="gene_name_key" type="text" value="gene_name" label="The key of the gene name in the gene annotation file"/> <param argument="gene_id_key" type="text" value="gene_id" label="The key of the gene id in the gene annotation file"/> <expand macro="min_max_frag_size"/> - <!--expand macro="param_counting_strategy"/--> - <param argument="count_frag_as_reads" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Whether to count fragments as reads"/> + <expand macro="param_counting_strategy"/> </when> <when value="pp.filter_cells"> <expand macro="inputs_anndata"/> @@ -446,7 +442,7 @@ <param name="transcript_id_key" value="transcript_id"/> <param name="gene_name_key" value="gene_name"/> <param name="gene_id_key" value="gene_id"/> - <param name="count_frag_as_reads" value="True"/> + <param name="counting_strategy" value="insertion"/> </conditional> <section name="advanced_common"> <param name="show_log" value="true" /> @@ -461,7 +457,7 @@ <has_text_matching expression="transcript_id_key = 'transcript_id'"/> <has_text_matching expression="gene_name_key = 'gene_name'"/> <has_text_matching expression="gene_id_key = 'gene_id'"/> - <has_text_matching expression="count_frag_as_reads = True"/> + <has_text_matching expression="counting_strategy = 'insertion'"/> </assert_contents> </output> <output name="anndata_out" location="https://zenodo.org/records/12548681/files/pp.make_gene_matrix.pbmc_500_chr21.h5ad" ftype="h5ad" compare="sim_size" delta_frac="0.1" /> @@ -513,7 +509,7 @@ <param name="bin_size" value="5000"/> <param name="chunk_size" value="500"/> <param name="exclude_chroms" value="chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr22, chrX, chrY"/> - <param name="count_frag_as_reads" value="True"/> + <param name="counting_strategy" value="insertion"/> </conditional> <section name="advanced_common"> <param name="show_log" value="true" /> @@ -524,7 +520,31 @@ <has_text_matching expression="bin_size = 5000"/> <has_text_matching expression="chunk_size = 500"/> <has_text_matching expression="exclude_chroms = \['chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chr20', 'chr22', 'chrX', 'chrY'\]"/> - <has_text_matching expression="count_frag_as_reads = True"/> + <has_text_matching expression="counting_strategy = 'insertion'"/> + </assert_contents> + </output> + <output name="anndata_out" ftype="h5ad" compare="sim_size" delta_frac="0.1" location="https://zenodo.org/records/11260316/files/pp.add_tile_matrix.pbmc_500_chr21.h5ad"/> + </test> + <test expect_num_outputs="2"> + <!-- pp.add_tile_matrix counting_strategy fragment --> + <conditional name="method"> + <param name="method" value="pp.add_tile_matrix"/> + <param name="adata" location="https://zenodo.org/records/11260316/files/pp.filter_cells.pbmc_500_chr21.h5ad"/> + <param name="bin_size" value="5000"/> + <param name="chunk_size" value="500"/> + <param name="exclude_chroms" value="chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr22, chrX, chrY"/> + <param name="counting_strategy" value="fragment"/> + </conditional> + <section name="advanced_common"> + <param name="show_log" value="true" /> + </section> + <output name="hidden_output"> + <assert_contents> + <has_text_matching expression="sa.pp.add_tile_matrix"/> + <has_text_matching expression="bin_size = 5000"/> + <has_text_matching expression="chunk_size = 500"/> + <has_text_matching expression="exclude_chroms = \['chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chr20', 'chr22', 'chrX', 'chrY'\]"/> + <has_text_matching expression="counting_strategy = 'fragment'"/> </assert_contents> </output> <output name="anndata_out" ftype="h5ad" compare="sim_size" delta_frac="0.1" location="https://zenodo.org/records/11260316/files/pp.add_tile_matrix.pbmc_500_chr21.h5ad"/> |