Mercurial > repos > iuc > snapatac2_plotting
diff macros.xml @ 6:1ac4a5f05f33 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
| author | iuc |
|---|---|
| date | Tue, 25 Nov 2025 16:41:12 +0000 |
| parents | 05bd4db20227 |
| children |
line wrap: on
line diff
--- a/macros.xml Thu Nov 07 13:07:52 2024 +0000 +++ b/macros.xml Tue Nov 25 16:41:12 2025 +0000 @@ -1,7 +1,7 @@ <macros> - <token name="@TOOL_VERSION@">2.6.4</token> - <token name="@VERSION_SUFFIX@">1</token> - <token name="@PROFILE@">23.0</token> + <token name="@TOOL_VERSION@">2.8.0</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@PROFILE@">24.0</token> <xml name="xrefs"> <xrefs> <xref type="bio.tools">snapatac</xref> @@ -9,168 +9,74 @@ </xml> <xml name="requirements"> <requirement type="package" version="@TOOL_VERSION@">snapatac2</requirement> - <requirement type="package" version="5.22.0">plotly</requirement> - <requirement type="package" version="0.2.1">python-kaleido</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> - <requirement type="package" version="0.10.2">leidenalg</requirement> + <requirement type="package" version="0.8.37">hdbscan</requirement> + <requirement type="package" version="0.10.2">leidenalg</requirement> + <requirement type="package" version="0.5.7">umap-learn</requirement> + <requirement type="package" version="3.0.4">xgboost</requirement> + <requirement type="package" version="0.2.1">python-kaleido</requirement> + <requirement type="package" version="1.31.0">polars</requirement> + <requirement type="package" version="5.24.1">plotly</requirement> + <requirement type="package" version="0.2.1">python-kaleido</requirement> + <requirement type="package" version="0.0.10">harmonypy</requirement> + <requirement type="package" version="1.7.4">scanorama</requirement> <yield /> </xml> - <token name="@PREP_ADATA@"><![CDATA[ + <!-- command section --> + <token name="@CMD_PREP_ADATA@"><![CDATA[ + ## ln -s does not work here cp '$method.adata' 'anndata.h5ad' && - ]]> - </token> - + ]]></token> <token name="@CMD@"><![CDATA[ cat '$script_file' > '$hidden_output' && python '$script_file' >> '$hidden_output' && touch 'anndata_info.txt' && - cat 'anndata_info.txt' @CMD_prettify_stdout@ - ]]> - </token> - - <token name="@CMD_prettify_stdout@"><![CDATA[ | sed -r '1 s|AnnData object with (.+) = (.*)\s*|\1: \2|g' | sed "s|'||g" | sed -r 's|^\s*(.*):\s(.*)|[\1]\n- \2|g' | sed 's|, |\n- |g' + cat 'anndata_info.txt' @CMD_PRETTIFY_STDOUT@ + ]]></token> + <token name="@CMD_PRETTIFY_STDOUT@"><![CDATA[ + | sed -r '1 s|AnnData object with (.+) = (.*)\s*|\1: \2|g' | sed "s|'||g" | sed -r 's|^\s*(.*):\s(.*)|[\1]\n- \2|g' | sed 's|, |\n- |g' + ]]></token> + <token name="@CMD_GET_GFF@"><![CDATA[ + #if $method.gff_file_condi.gffSource == 'cached': + ln -s '$method.gff_file_condi.gff_pre_installed.fields.path' gff && + #else: + ln -s '$method.gff_file_condi.gff_history' gff && + #end if + ]]></token> + <token name="@CMD_GET_FASTA@"><![CDATA[ + #if $method.fasta_file_condi.fastaSource == 'indexed': + zcat '$method.fasta_file_condi.fasta_pre_installed.fields.path' > fasta.fa && + echo "Using built-in FASTA: '$method.fasta_file_condi.fasta_pre_installed.fields.name'" >&2 && + #else: + #if $method.fasta_file_condi.fasta_history.ext.endswith('.gz') + zcat '$method.fasta_file_condi.fasta_history' > fasta.fa && + #else: + ln -s '$method.fasta_file_condi.fasta_history' fasta.fa && + #end if + #end if ]]></token> - <token name="@CMD_imports@"><![CDATA[ -import snapatac2 as sa + <!-- Config section --> + <token name="@CONF_IMPORTS@"><![CDATA[ +import snapatac2 as snap import os - ]]> - </token> - <xml name="sanitize_query" token_validinitial="string.printable"> - <sanitizer> - <valid initial="@VALIDINITIAL@"> - <remove value="'" /> - </valid> - </sanitizer> - </xml> - - <xml name="inputs_anndata"> - <param name="adata" type="data" format="h5ad" label="Annotated data matrix"/> - </xml> - - <token name="@CMD_read_inputs@"><![CDATA[ - -adata = sa.read('anndata.h5ad', backed = None) -]]> - </token> - - <xml name="dimentions_plot"> - <param argument="width" type="integer" value="500" label="Width of the plot"/> - <param argument="height" type="integer" value="400" label="Height of the plot"/> - </xml> - - <xml name="param_groupby"> - <param argument="groupby" type="text" label="The key of the observation grouping to consider"> - <expand macro="sanitize_query" /> - </param> - </xml> - - <xml name="out_file"> - <param name="out_file" type="select" optional="true" label="Type of output plot"> - <option value="png" selected="true">PNG</option> - <option value="svg">SVG</option> - <option value="pdf">PDF</option> - </param> - </xml> - <token name="@CMD_anndata_write_outputs@"><![CDATA[ -adata.write('anndata.h5ad') + ]]></token> + <token name="@CONF_READ_INPUTS@"><![CDATA[ +adata = snap.read('anndata.h5ad', backed = None) + ]]></token> + <token name="@CONF_ANNDATA_WRITE_OUTPUTS@"><![CDATA[ +adata.write_h5ad('anndata.h5ad.gz', compression='gzip') with open('anndata_info.txt','w', encoding='utf-8') as ainfo: print(adata, file=ainfo) -]]> - </token> - <xml name="inputs_common_advanced"> - <section name="advanced_common" title="Advanced Options" expanded="false"> - <param name="show_log" type="boolean" checked="false" label="Output Log?" /> - </section> - </xml> - <xml name="params_render_plot"> - <param argument="width" type="integer" value="600" label="Width of the plot"/> - <param argument="height" type="integer" value="400" label="Height of the plot"/> - <expand macro="out_file"/> - </xml> - <xml name="param_shift"> - <param argument="shift_left" type="integer" value="4" label="Insertion site correction for the left end" help="Note this has no effect on single-end reads"/> - <param argument="shift_right" type="integer" value="-5" label="Insertion site correction for the right end" help="Note this has no effect on single-end reads"/> - </xml> - <xml name="param_chunk_size" tokens="size"> - <param argument="chunk_size" type="integer" value="@SIZE@" label="chunk size"/> - </xml> - <xml name="min_max_frag_size"> - <param argument="min_frag_size" type="integer" optional="true" value="" label="Minimum fragment size to include"/> - <param argument="max_frag_size" type="integer" optional="true" value="" label="Maximum fragment size to include"/> - </xml> - <xml name="params_data_integration"> - <param argument="use_rep" type="text" value="X_spectral" label="The key for the matrix"/> - <param argument="use_dims" type="text" optional="true" value="" label="The dimensions used for computation"> - <expand macro="sanitize_query"/> - </param> - <param argument="groupby" type="text" optional="true" value="" label="The key of the observation grouping to consider"> - <expand macro="sanitize_query" /> - </param> - <param argument="key_added" type="text" optional="true" value="" label="If specified, add the result to adata.obsm with this key"/> - </xml> - <xml name="param_n_comps"> - <param argument="n_comps" type="integer" value="30" label="Number of dimensions to keep" help="The result is insensitive to this parameter when `weighted_by_sd` is set, as long as it is large enough, e.g. 30."/> - </xml> - <xml name="param_random_state"> - <param argument="random_state" type="integer" value="0" label="Seed of the random state generator"/> - </xml> - <xml name="param_key_added" tokens="key_added"> - <param argument="key_added" type="text" value="@KEY_ADDED@" label="`adata.obs` key under which t add cluster labels"/> - </xml> - <xml name="param_use_rep"> - <param argument="use_rep" type="text" value="X_spectral" label="Use the indicated representation in `.obsm`"/> - </xml> - <xml name="genome_fasta"> - <param argument="genome_fasta" type="text" label="A fasta file containing the genome sequences or a Genome object"/> - </xml> - <xml name="background"> - <param argument="background" type="text" optional="true" value="" label="A list of regions to be used as the background"> - <expand macro="sanitize_query"/> - </param> - </xml> - <xml name="mat"> - <param argument="peak_mat" type="data" format="h5ad" optional="true" label="AnnData or AnnDataSet object storing the cell by peak count matrix"/> - <param argument="gene_mat" type="data" format="h5ad" optional="true" label="AnnData or AnnDataSet object storing the cell by gene count matrix"/> - </xml> - <xml name="param_network"> - <param argument="network" type="text" label="network"/> - </xml> - <xml name="param_n_iterations"> - <param argument="n_iterations" type="integer" value="-1" label="How many iterations of the Leiden clustering algorithm to perform" - help="Positive values above 2 define the total number of iterations to perform, -1 has the algorithm run until it reaches its optimal clustering."/> - </xml> - - <xml name="citations"> - <citations> - <citation type="doi">10.1038/s41592-023-02139-9</citation> - </citations> - </xml> - <xml name="render_plot_test"> - <param name="width" value="650"/> - <param name="height" value="450"/> - </xml> - <xml name="render_plot_matching_text"> - <has_text_matching expression="width = 650"/> - <has_text_matching expression="height = 450"/> - </xml> - <xml name="param_counting_strategy"> - <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> - - <token name="@CMD_params_data_integration@"><![CDATA[ + ]]></token> + <token name="@CONF_PARAMS_RENDER_PLOT@"><![CDATA[ + width = $method.width, + height = $method.height, + show = False, + interactive = False, + out_file = 'plot.$method.out_file', + ]]></token> + <token name="@CONF_PARAMS_DATA_INTEGRATION@"><![CDATA[ use_rep = '$method.use_rep', #if $method.use_dims != '' #set $dims = ([x.strip() for x in str($method.use_dims).split(',')]) @@ -183,13 +89,168 @@ #if $method.key_added != '' key_added = '$method.key_added', #end if - ]]> - </token> + ]]></token> + <token name="@CONF_IMPORT_MEME@"><![CDATA[ +motifs = read_motifs("input.meme") +for motif in motifs: + motif.name = motif.id.split('+')[0] + +unique_motifs = {} +for motif in motifs: + name = motif.name + if ( + name not in unique_motifs or + unique_motifs[name].info_content() < motif.info_content() + ): + unique_motifs[name] = motif +motifs = list(unique_motifs.values()) + + +#else: +motifs = read_motifs("input.meme") +for motif in motifs: + motif.name = motif.id.split('_')[0] + motif.family = motif.id.split('+')[-1] + ]]></token> + + <!-- input section --> + <xml name="sanitize_query" token_validinitial="string.printable"> + <sanitizer> + <valid initial="@VALIDINITIAL@"> + <remove value="'" /> + <yield/> + </valid> + </sanitizer> + </xml> - <token name="@CMD_params_render_plot@"><![CDATA[ - width = $method.width, - height = $method.height, - out_file = 'plot.$method.out_file', - ]]> - </token> + <xml name="param_inputs_anndata" token_multiple="false" token_label="Annotated data matrix"> + <param name="adata" type="data" multiple="@MULTIPLE@" format="h5ad" label="@LABEL@"/> + </xml> + <xml name="param_groupby"> + <param argument="groupby" type="text" label="The key of the observation grouping to consider"> + <expand macro="sanitize_query" /> + </param> + </xml> + <xml name="param_common_advanced"> + <section name="advanced_common" title="Advanced Options" expanded="false"> + <param name="show_log" type="boolean" checked="false" label="Output Log?" /> + </section> + </xml> + <xml name="param_render_plot"> + <param argument="width" type="integer" value="600" label="Width of the plot"/> + <param argument="height" type="integer" value="400" label="Height of the plot"/> + <param name="out_file" type="select" optional="true" label="Type of output plot"> + <option value="png" selected="true">PNG</option> + <option value="svg">SVG</option> + <option value="pdf">PDF</option> + <option value="html">HTML</option> + </param> + </xml> + <xml name="param_shift" tokens="varname" token_value="0" token_label="Insertion site correction for the left end"> + <param argument="@VARNAME@" type="integer" value="@VALUE@" label="@LABEL@" help="Note this has no effect on single-end reads"/> + </xml> + <xml name="param_chunk_size" tokens="size"> + <param argument="chunk_size" type="integer" value="@SIZE@" label="chunk size"/> + </xml> + <xml name="param_min_max_frag_size"> + <param argument="min_frag_size" type="integer" optional="true" value="" label="Minimum fragment size to include"/> + <param argument="max_frag_size" type="integer" optional="true" value="" label="Maximum fragment size to include"/> + </xml> + <xml name="param_data_integration"> + <param argument="use_rep" type="text" value="X_spectral" label="The key for the matrix"/> + <param argument="use_dims" type="text" optional="true" value="" label="The dimensions used for computation"> + <expand macro="sanitize_query"/> + </param> + <param argument="groupby" type="text" optional="true" value="" label="The key of the observation grouping to consider"> + <expand macro="sanitize_query" /> + </param> + <param argument="key_added" type="text" optional="true" value="" label="If specified, add the result to adata.obsm with this key"/> + </xml> + <xml name="param_random_state" token_label="Seed of the random state generator" token_help=""> + <param argument="random_state" type="integer" value="0" label="@LABEL@" help="@HELP@"/> + </xml> + <xml name="param_key_added" tokens="key_added"> + <param argument="key_added" type="text" value="@KEY_ADDED@" label="`adata.obs` key under which t add cluster labels"/> + </xml> + <xml name="param_use_rep" token_label="Use the indicated representation in `.obsm`"> + <param argument="use_rep" type="text" value="X_spectral" label="@LABEL@"/> + </xml> + <xml name="param_n_iterations"> + <param argument="n_iterations" type="integer" value="-1" label="How many iterations of the Leiden clustering algorithm to perform" + help="Positive values above 2 define the total number of iterations to perform, -1 has the algorithm run until it reaches its optimal clustering."/> + </xml> + <xml name="param_counting_strategy"> + <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">"insertion": based on the number of insertions that overlap with a region of interest</option> + <option value="paired-insertion" selected="true">"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> + <xml name="param_chrom_sizes"> + <param argument="chrom_sizes" type="data" format="tabular" label="Chromosome sizes" help="First column the chromosome name and second column the size"/> + </xml> + <xml name="param_genome_fasta"> + <conditional name="fasta_file_condi"> + <param name="fastaSource" type="select" label="Select a built-in FASTA or one from your history" help="Choose history if you don't see the correct FASTA."> + <option value="indexed" selected="true">Use a built-in FASTA</option> + <option value="history">Use a FASTA from history</option> + </param> + <when value="indexed"> + <param name="fasta_pre_installed" type="select" label="Select a FASTA file" help="Select the FASTA file from a list of pre-installed genomes"> + <options from_data_table="all_fasta"> + <filter type="sort_by" column="2" /> + </options> + </param> + </when> + <when value="history"> + <param name="fasta_history" type="data" format="fasta,fasta.gz" label="FASTA file" /> + </when> + </conditional> + </xml> + <xml name="param_gene_anno"> + <conditional name="gff_file_condi"> + <param name="gffSource" type="select" label="Select a built-in GFF file or one from your history" help="Choose history if you don't see the correct GFF" > + <option value="cached" selected="true">Use a built-in GFF</option> + <option value="history">Use a GFF from history</option> + </param> + <when value="cached"> + <param name="gff_pre_installed" type="select" label="Select a GFF file" help="Select the GFF from a list of pre-installed files"> + <options from_data_table="gene_sets"> + <filter type="sort_by" column="1" /> + </options> + </param> + </when> + <when value="history"> + <param name="gff_history" type="data" format="gff3.gz" label="Select a GFF file" help="Make sure that the GFF corresponds to the same genome as the FASTA"/> + </when> + </conditional> + </xml> + <xml name="param_n_comps" token_value="30" token_label="Number of dimensions to keep" token_help="The result is insensitive to this parameter when `weighted_by_sd` is set, as long as it is large enough, e.g. 30."> + <param argument="n_comps" type="integer" value="@VALUE@" label="@LABEL@" help="@HELP@"/> + </xml> + <xml name="param_meme_table"> + <param name="motifs" type="select" label="Select list of transcription factor motifs"> + <options from_data_table="meme"> + <filter type="sort_by" column="2" /> + </options> + </param> + </xml> + + + <!-- test section --> + <xml name="test_param_render_plot"> + <param name="width" value="650"/> + <param name="height" value="450"/> + </xml> + <xml name="test_render_plot_matching_text"> + <has_text_matching expression="width = 650"/> + <has_text_matching expression="height = 450"/> + </xml> + + + <xml name="citations"> + <citations> + <citation type="doi">10.1038/s41592-023-02139-9</citation> + </citations> + </xml> </macros>