Mercurial > repos > iuc > snapatac2_plotting
changeset 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 | |
| files | macros.xml plotting.xml test-data/all_fasta.loc test-data/chr21.gff3.gz test-data/chr21_small.fasta.gz test-data/cisBP_human.meme.gz test-data/gene_sets.loc test-data/meme.loc tool-data/all_fasta.loc.sample tool-data/gene_sets.loc.sample tool-data/meme.loc.sample tool_data_table_conf.xml.sample tool_data_table_conf.xml.test |
| diffstat | 13 files changed, 359 insertions(+), 214 deletions(-) [+] |
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--- 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>
--- a/plotting.xml Thu Nov 07 13:07:52 2024 +0000 +++ b/plotting.xml Tue Nov 25 16:41:12 2025 +0000 @@ -7,30 +7,31 @@ <expand macro="requirements"/> </requirements> <command detect_errors="exit_code"><![CDATA[ -@PREP_ADATA@ +@CMD_PREP_ADATA@ @CMD@ ]]></command> <configfiles> <configfile name="script_file"><![CDATA[ -@CMD_imports@ -@CMD_read_inputs@ +@CONF_IMPORTS@ +@CONF_READ_INPUTS@ #if $method.method == 'pl.frag_size_distr' #if $method.log_scale -fig = sa.pl.frag_size_distr(adata, show=False) +fig = snap.pl.frag_size_distr(adata, show=False) fig.update_yaxes(type="log") -sa.pl.render_plot(fig, @CMD_params_render_plot@) +snap.pl.render_plot(fig, @CONF_PARAMS_RENDER_PLOT@) #else -sa.pl.frag_size_distr(adata, @CMD_params_render_plot@) +snap.pl.frag_size_distr(adata, @CONF_PARAMS_RENDER_PLOT@) #end if + #else if $method.method == 'pl.tsse' -sa.pl.tsse( +snap.pl.tsse( adata, min_fragment = $method.min_fragment, - @CMD_params_render_plot@ + @CONF_PARAMS_RENDER_PLOT@ ) #else if $method.method == 'pl.umap' -sa.pl.umap( +snap.pl.umap( adata, color = '$method.color', use_rep = '$method.use_rep', @@ -41,19 +42,13 @@ #if $method.sample_size sample_size = $method.sample_size, #end if - @CMD_params_render_plot@ + @CONF_PARAMS_RENDER_PLOT@ ) -#else if $method.method == 'pl.regions' -sa.pl.regions( + +#else if $method.method == 'pl.spectral_eigenvalues' +snap.pl.spectral_eigenvalues( adata, - groupby = '$method.groupby', - peaks = '$method.peaks', - @CMD_params_render_plot@ -) -#else if $method.method == 'pl.spectral_eigenvalues' -sa.pl.spectral_eigenvalues( - adata, - @CMD_params_render_plot@ + @CONF_PARAMS_RENDER_PLOT@ ) #end if ]]></configfile> @@ -67,30 +62,31 @@ <option value="pl.spectral_eigenvalues">Plot the eigenvalues of spectral embedding, using 'pl.spectral_eigenvalues'</option> </param> <when value="pl.frag_size_distr"> - <expand macro="inputs_anndata"/> + <expand macro="param_inputs_anndata"/> + <param argument="use_rep" type="text" value="frag_size_distr" label="Use the indicated representation in .obsm"/> <param name="log_scale" type="boolean" checked="False" label="Change the y-axis (fragment counts) to log scale"/> - <expand macro="params_render_plot"/> + <expand macro="param_render_plot"/> </when> <when value="pl.tsse"> - <expand macro="inputs_anndata"/> + <expand macro="param_inputs_anndata"/> <param argument="min_fragment" type="integer" value="500" label="Minimum number of unique fragments"/> - <expand macro="params_render_plot"/> + <expand macro="param_render_plot"/> </when> <when value="pl.umap"> - <expand macro="inputs_anndata"/> - <param argument="color" type="text" value="" optional="true" label="Color"/> + <expand macro="param_inputs_anndata"/> + <param argument="color" type="text" value="" optional="true" label="Color" help="Color to use for the points. retrieved from .obs"/> <param argument="use_rep" type="text" value="X_umap" label="Use the indicated representation in .obsm"/> <param argument="marker_size" type="float" value="" optional="true" label="Size of the dots"/> - <param argument="marker_opacity" type="float" value="1" label="Opactiy of the dots"/> + <param argument="marker_opacity" type="float" value="1" label="Opacity of the dots"/> <param argument="sample_size" type="integer" value="" optional="true" label="Number of cells to use"/> - <expand macro="params_render_plot"/> + <expand macro="param_render_plot"/> </when> <when value="pl.spectral_eigenvalues"> - <expand macro="inputs_anndata"/> - <expand macro="params_render_plot"/> + <expand macro="param_inputs_anndata"/> + <expand macro="param_render_plot"/> </when> </conditional> - <expand macro="inputs_common_advanced"/> + <expand macro="param_common_advanced"/> </inputs> <outputs> <data name="out_png" format="png" from_work_dir="plot.png" label="PNG plot from ${tool.name} (${method.method}) on ${on_string}"> @@ -102,6 +98,9 @@ <data name="out_svg" format="svg" from_work_dir="plot.svg" label="SVG plot from ${tool.name} (${method.method}) on ${on_string}"> <filter>method['out_file'] == 'svg'</filter> </data> + <data name="out_html" format="html" from_work_dir="plot.html" label="HTML plot from ${tool.name} (${method.method}) on ${on_string}"> + <filter>method['out_file'] == 'html'</filter> + </data> <data name="hidden_output" format="txt" label="Log file" hidden="true"> <filter>advanced_common['show_log']</filter> </data> @@ -111,20 +110,20 @@ <!-- pl.frag_size_distr --> <conditional name="method"> <param name="method" value="pl.frag_size_distr"/> - <param name="adata" location="https://zenodo.org/records/11260316/files/pp.import_data.pbmc_500_chr21.h5ad"/> + <param name="adata" location="https://zenodo.org/records/17512085/files/pp.import_data.pbmc_500_chr21.h5ad"/> <param name="log_scale" value="True"/> <param name="out_file" value="pdf"/> - <expand macro="render_plot_test"/> + <expand macro="test_param_render_plot"/> </conditional> <section name="advanced_common"> <param name="show_log" value="true"/> </section> - <output name="out_pdf" location="https://zenodo.org/records/11260316/files/pl.frag_size_distr.pdf" ftype="pdf" compare="sim_size" delta_frac="0.1"/> + <output name="out_pdf" location="https://zenodo.org/records/17512085/files/pl.frag_size_distr.pdf" ftype="pdf" compare="sim_size" delta_frac="0.1"/> <output name="hidden_output"> <assert_contents> - <has_text_matching expression="sa.pl.frag_size_distr"/> + <has_text_matching expression="snap.pl.frag_size_distr"/> <has_text_matching expression="fig.update_yaxes"/> - <expand macro="render_plot_matching_text"/> + <expand macro="test_render_plot_matching_text"/> </assert_contents> </output> </test> @@ -132,34 +131,41 @@ <!-- pl.tsse --> <conditional name="method"> <param name="method" value="pl.tsse"/> - <param name="adata" location="https://zenodo.org/records/11260316/files/metrics.tsse.pbmc_500_chr21.h5ad"/> + <param name="adata" location="https://zenodo.org/records/17512085/files/metrics.tsse.pbmc_500_chr21.h5ad"/> <param name="min_fragment" value="500"/> <param name="out_file" value="png"/> - <expand macro="render_plot_test"/> + <expand macro="test_param_render_plot"/> </conditional> <section name="advanced_common"> <param name="show_log" value="true"/> </section> <output name="hidden_output"> <assert_contents> - <has_text_matching expression="sa.pl.tsse"/> + <has_text_matching expression="snap.pl.tsse"/> <has_text_matching expression="min_fragment = 500"/> - <expand macro="render_plot_matching_text"/> + <expand macro="test_render_plot_matching_text"/> </assert_contents> </output> - <output name="out_png" location="https://zenodo.org/records/11260316/files/pl.tsse.png" ftype="png" compare="sim_size" delta_frac="0.1"/> + <output name="out_png"> + <assert_contents> + <has_image_center_of_mass center_of_mass="325,223" eps="30"/> + <has_image_channels channels="4"/> + <has_image_height height="450"/> + <has_image_width width="650"/> + </assert_contents> + </output> </test> <test expect_num_outputs="2"> <!-- pl.umap --> <conditional name="method"> <param name="method" value="pl.umap"/> - <param name="adata" ftype="h5ad" location="https://zenodo.org/records/11260316/files/tl.leiden.modularity.pbmc_500_chr21.h5ad"/> + <param name="adata" ftype="h5ad" location="https://zenodo.org/records/17512085/files/tl.leiden.modularity.pbmc_500_chr21.h5ad"/> <param name="color" value="leiden"/> <param name="use_rep" value="X_umap"/> <param name="marker_size" value="1"/> <param name="marker_opacity" value="0.8"/> <param name="sample_size" value="100"/> - <expand macro="render_plot_test"/> + <expand macro="test_param_render_plot"/> <param name="out_file" value="svg"/> </conditional> <section name="advanced_common"> @@ -167,23 +173,23 @@ </section> <output name="hidden_output"> <assert_contents> - <has_text_matching expression="sa.pl.umap"/> + <has_text_matching expression="snap.pl.umap"/> <has_text_matching expression="color = 'leiden'"/> <has_text_matching expression="use_rep = 'X_umap'"/> <has_text_matching expression="marker_size = 1"/> <has_text_matching expression="marker_opacity = 0.8"/> <has_text_matching expression="sample_size = 100"/> - <expand macro="render_plot_matching_text"/> + <expand macro="test_render_plot_matching_text"/> </assert_contents> </output> - <output name="out_svg" location="https://zenodo.org/records/11260316/files/pl.umap.svg" ftype="svg" compare="sim_size" delta_frac="0.1"/> + <output name="out_svg" location="https://zenodo.org/records/17512085/files/pl.umap.svg" ftype="svg" compare="sim_size" delta_frac="0.1"/> </test> <test expect_num_outputs="2"> <!-- pl.spectral_eigenvalues --> <conditional name="method"> <param name="method" value="pl.spectral_eigenvalues"/> - <param name="adata" ftype="h5ad" location="https://zenodo.org/records/11260316/files/tl.spectral.pbmc_500_chr21.h5ad"/> - <expand macro="render_plot_test"/> + <param name="adata" ftype="h5ad" location="https://zenodo.org/records/17512085/files/tl.spectral.pbmc_500_chr21.h5ad"/> + <expand macro="test_param_render_plot"/> <param name="out_file" value="pdf"/> </conditional> <section name="advanced_common"> @@ -191,11 +197,11 @@ </section> <output name="hidden_output"> <assert_contents> - <has_text_matching expression="sa.pl.spectral_eigenvalues"/> - <expand macro="render_plot_matching_text"/> + <has_text_matching expression="snap.pl.spectral_eigenvalues"/> + <expand macro="test_render_plot_matching_text"/> </assert_contents> </output> - <output name="out_pdf" location="https://zenodo.org/records/11260316/files/pl.spectral_eigenvalues.pdf" ftype="pdf" compare="sim_size" delta_frac="0.1"/> + <output name="out_pdf" location="https://zenodo.org/records/17512085/files/pl.spectral_eigenvalues.pdf" ftype="pdf" compare="sim_size" delta_frac="0.1"/> </test> </tests> <help><![CDATA[ @@ -212,7 +218,7 @@ Plot the TSS enrichment vs. number of fragments density figure. More details on the `SnapATAC2 documentation -<https://kzhang.org/SnapATAC2/api/_autosummary/snapatac2.pl.tsse.html>`__ +<https://scverse.org/SnapATAC2/api/_autosummary/snapatac2.pl.tsse.html>`__ Plot the UMAP embedding, using `pl.umap` ======================================== @@ -220,7 +226,7 @@ Plot the UMAP embedding. More details on the `SnapATAC2 documentation -<https://kzhang.org/SnapATAC2/api/_autosummary/snapatac2.pl.umap.html>`__ +<https://scverse.org/SnapATAC2/api/_autosummary/snapatac2.pl.umap.html>`__ Plot the eigenvalues of spectral embedding, using `pl.spectral_eigenvalues` =========================================================================== @@ -228,7 +234,7 @@ Plot the eigenvalues of spectral embedding. More details on the `SnapATAC2 documentation -<https://kzhang.org/SnapATAC2/api/_autosummary/snapatac2.pl.spectral_eigenvalues.html>`__ +<https://scverse.org/SnapATAC2/api/_autosummary/snapatac2.pl.spectral_eigenvalues.html>`__ ]]></help> <expand macro="citations"/> </tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/all_fasta.loc Tue Nov 25 16:41:12 2025 +0000 @@ -0,0 +1,1 @@ +hg38 hg38 Human (hg38) ${__HERE__}/chr21_small.fasta.gz \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gene_sets.loc Tue Nov 25 16:41:12 2025 +0000 @@ -0,0 +1,1 @@ +hg38 hg38 hg38GFF ${__HERE__}/chr21.gff3.gz \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/meme.loc Tue Nov 25 16:41:12 2025 +0000 @@ -0,0 +1,1 @@ +cisbp snap.datasets.cis_bp(unique=True) ${__HERE__}/cisBP_human.meme.gz \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/all_fasta.loc.sample Tue Nov 25 16:41:12 2025 +0000 @@ -0,0 +1,17 @@ +#This file lists the locations and dbkeys of all the genome and transcriptome fasta files +#under the "genome" directory (a directory that contains a directory +#for each build. This file has the format (white space characters are +#TAB characters): +# +#<unique_build_id> <dbkey> <display_name> <file_path> +# +#So, all_fasta.loc could look something like this: +# +#apiMel4.5 apiMel4.5 Honeybee (Apis mellifera): apiMel4.5 /path/to/genome/apiMel4.5/apiMel4.5.fa +#hg38canon hg38 Human (Homo sapiens): hg38 Canonical /path/to/genome/hg38/hg38canon.fa +#hg38full hg38 Human (Homo sapiens): hg38 Full /path/to/genome/hg38/hg38full.fa +#hg38full.90 hg38 Human (Homo sapiens): hg38 Full Trans v90 /path/to/genome/hg38/hg38fulltrans.fa + +#Your all_fasta.loc file should contain an entry for each individual +#fasta file. So there will be multiple fasta files for each build, +#such as with hg38 above. \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/gene_sets.loc.sample Tue Nov 25 16:41:12 2025 +0000 @@ -0,0 +1,14 @@ +# This is a sample file distributed with featureCounts that enables it and other# tools to use gene/exon annotations in the GFF/GTF format. +# +# The gene_sets.loc file syntax is: +#<unique_build_id> <dbkey> <display_name> <path> +# +# Please ensure that the above fields are tab separated. +# +# In case you have TWO or MORE providers PER dbkey, the one mentioned +# first in the file, should have the "default" priority. +# +#Example: +# +#Homo_sapiens.GRCh38.90 hg38 GRCh38 (hg38) annotation from Ensembl, release 90 /depot/data2/galaxy/hg38/gene_sets/Homo_sapiens.GRCh38.90.gtf +#Homo_sapiens.GRCh37.87 hg19 GRCh37 (hg19) annotation from Ensembl, release 87 /depot/data2/galaxy/hg19/gene_sets/Homo_sapiens.GRCh37.87.gtf \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/meme.loc.sample Tue Nov 25 16:41:12 2025 +0000 @@ -0,0 +1,13 @@ +# This is a sample file distributed with snapatac2 which enables the tool to perform motif enrichment analysis +# +# The meme.loc file syntax is: +#<unique_id> <display_name> <path> +# +# Please ensure that the above fields are tab separated. +# +# Currently the files should be downloaded manually +# +#Example: +# +#cisbp cis_bp(unique=True) /path/to/cisBP_human.meme.gz +#meuleman_2020 Meuleman_2020 /path/to/Meuleman_2020.meme.gz \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Tue Nov 25 16:41:12 2025 +0000 @@ -0,0 +1,17 @@ +<tables> + <!-- Locations of all fasta files under genome directory --> + <table name="all_fasta" comment_char="#" allow_duplicate_entries="False"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/all_fasta.loc" /> + </table> + <!-- Locations of all gff files with annotations of genome builds --> + <table name="gene_sets" comment_char="#" allow_duplicate_entries="False"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/gene_sets.loc" /> + </table> + <!-- Locations of all meme files --> + <table name="meme" comment_char="#" allow_duplicate_entries="False"> + <columns>value, name, path</columns> + <file path="tool-data/meme.loc" /> + </table> +</tables> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Tue Nov 25 16:41:12 2025 +0000 @@ -0,0 +1,14 @@ +<tables> + <table name="all_fasta" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="${__HERE__}/test-data/all_fasta.loc" /> + </table> + <table name="gene_sets" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="${__HERE__}/test-data/gene_sets.loc" /> + </table> + <table name="meme" comment_char="#"> + <columns>value, name, path</columns> + <file path="${__HERE__}/test-data/meme.loc" /> + </table> +</tables> \ No newline at end of file