Mercurial > repos > iuc > snapatac2_peaks_and_motif
changeset 2:b9013e0e2b00 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984
| author | iuc |
|---|---|
| date | Wed, 17 Jul 2024 05:54:41 +0000 |
| parents | f9647da40db3 |
| children | 88192fe25375 |
| files | macros.xml peaks_and_motif_analysis.xml |
| diffstat | 2 files changed, 26 insertions(+), 20 deletions(-) [+] |
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--- a/macros.xml Fri Jul 05 11:06:04 2024 +0000 +++ b/macros.xml Wed Jul 17 05:54:41 2024 +0000 @@ -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>
--- a/peaks_and_motif_analysis.xml Fri Jul 05 11:06:04 2024 +0000 +++ b/peaks_and_motif_analysis.xml Wed Jul 17 05:54:41 2024 +0000 @@ -36,6 +36,9 @@ nolambda = $method.nolambda, shift = $method.shift, extsize = $method.extsize, + #if $method.min_len + min_len = $method.min_len, + #end if #if $method.blacklist blacklist = '$method.blacklist', #end if @@ -62,7 +65,7 @@ #else if $method.method == 'pp.make_peak_matrix' import polars peaks = polars.read_csv('$method.merged_peaks', separator='\t') -sa.pp.make_peak_matrix( +adata = sa.pp.make_peak_matrix( adata, use_rep = peaks['Peaks'], chunk_size = $method.chunk_size, @@ -73,8 +76,7 @@ #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 == 'tl.marker_regions' @@ -150,7 +152,9 @@ ) #end if +#if $method.method != 'pp.make_peak_matrix' @CMD_anndata_write_outputs@ +#end if ]]></configfile> </configfiles> <inputs> @@ -173,6 +177,7 @@ <param argument="nolambda" type="boolean" checked="false" truevalue="True" falsevalue="False" label="If True, macs3 will use the background lambda as local lambda"/> <param argument="shift" type="integer" value="-100" label="The shift size in MACS"/> <param argument="extsize" type="integer" value="200" label="The extension size in MACS"/> + <param argument="min_len" type="integer" optional="true" value="" label="The minimum length of a called peak" help="If not set, it is set to the extension size."/> <param argument="blacklist" type="data" format="bed" optional="true" label="Blacklist file in BED format" help="If provided, regions in the blacklist will be removed."/> <param argument="key_added" type="text" value="macs3" label="`.uns` key under which to add peak information"/> @@ -192,8 +197,7 @@ <expand macro="param_chunk_size" size="500"/> <param argument="use_x" type="boolean" truevalue="True" falsevalue="False" checked="false" label="If True, use the matrix stored in .X as raw counts"/> <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="tl.marker_regions"> <expand macro="inputs_anndata"/> @@ -264,6 +268,7 @@ <param name="qvalue" value="0.1"/> <param name="shift" value="-100"/> <param name="extsize" value="200"/> + <param name="min_len" value="50"/> <param name="key_added" value="macs3"/> </conditional> <section name="advanced_common"> @@ -276,6 +281,7 @@ <has_text_matching expression="qvalue = 0.1"/> <has_text_matching expression="shift = -100"/> <has_text_matching expression="extsize = 200"/> + <has_text_matching expression="min_len = 50"/> <has_text_matching expression="key_added = 'macs3'"/> </assert_contents> </output> @@ -317,7 +323,7 @@ <param name="merged_peaks" location="https://zenodo.org/records/11260316/files/merged_peaks.tabular"/> <param name="chunk_size" value="500"/> <param name="use_x" value="False"/> - <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" /> @@ -327,10 +333,10 @@ <has_text_matching expression="sa.pp.make_peak_matrix"/> <has_text_matching expression="chunk_size = 500"/> <has_text_matching expression="use_x = False"/> - <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/11260316/files/pp.make_peak_matrix.pbmc_500_chr21.h5ad" ftype="h5ad" compare="sim_size" delta_frac="0.1" /> + <output name="anndata_out" location="https://zenodo.org/records/12751925/files/pp.make_peak_matrix.pbmc_500_chr21.h5ad" ftype="h5ad" compare="sim_size" delta_frac="0.1" /> </test> <test expect_num_outputs="3"> <!-- tl.marker_regions -->