Mercurial > repos > iuc > episcanpy_build_matrix
changeset 1:31a21ba2c5ea draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit bb79cb8cad3bc1433bff7caf9d7b45e7993dd470
| author | iuc |
|---|---|
| date | Sat, 22 Apr 2023 12:14:00 +0000 |
| parents | 1bf008d6d54e |
| children | |
| files | build_matrix.xml macros.xml test-data/chrY.h5ad test-data/chrY_norm_peaks.h5ad test-data/chrY_with_transcript_annotation.h5ad |
| diffstat | 5 files changed, 32 insertions(+), 4 deletions(-) [+] |
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--- a/build_matrix.xml Tue Apr 18 13:19:11 2023 +0000 +++ b/build_matrix.xml Sat Apr 22 12:14:00 2023 +0000 @@ -18,7 +18,9 @@ <configfile name="script_file"><![CDATA[ @CMD_imports@ peaks = esc.ct.load_peaks('$peaks_file') -esc.ct.norm_peaks(peaks, extension=$extension) +#if $peak_size.normalize == 'yes' +esc.ct.norm_peaks(peaks, extension=$peak_size.extension) +#end if esc.ct.bld_mtx_bed( fragment_file='fragments.gz', feature_region=peaks, @@ -34,7 +36,16 @@ <inputs> <param name="fragment_file" type="data" format="bed" label="ATAC fragments file" /> <param name="peaks_file" type="data" format="tabular" label="Features file" help="Peaks BED file or MACS2 narrowPeak file"/> - <param name="extension" type="integer" value="0" min="0" label="Number of bases to extend both sides of peaks" /> + <conditional name="peak_size"> + <param name="normalize" type="select" label="Normalize peak sizes?" > + <option value="no" selected="true">No, keep the peaks as they are</option> + <option value="yes">Yes, normalize the peaks to equal length from the center</option> + </param> + <when value="no" /> + <when value="yes"> + <param name="extension" type="integer" value="0" min="0" label="Number of bases to extend both sides from the center of the peak" help="All resulting peaks will have the same length"/> + </when> + </conditional> <conditional name="reference_chr"> <param name="chr_select" type="select" label="Select the chromosomes of the species you are considering" > <option value="human">Human chromosomes ['1', '2', '3', ... , '22', 'X', 'Y']</option> @@ -59,7 +70,7 @@ </outputs> <tests> <test expect_num_outputs="2"> - <!-- count matrix --> + <!-- default params --> <param name="fragment_file" value="chrY.fragments.bed" /> <param name="peaks_file" value="chrY.peaks.bed" /> <conditional name="reference_chr"> @@ -71,6 +82,23 @@ </section> <output name="anndata_out" file="chrY.h5ad" ftype="h5ad" compare="sim_size"/> </test> + <test expect_num_outputs="2"> + <!-- normalized peaks --> + <param name="fragment_file" value="chrY.fragments.bed" /> + <param name="peaks_file" value="chrY.peaks.bed" /> + <conditional name="peak_size"> + <param name="normalize" value="yes" /> + <param name="extension" value="250" /> + </conditional> + <conditional name="reference_chr"> + <param name="chr_select" value="custom" /> + <param name="chromosomes" value="Y" /> + </conditional> + <section name="advanced_common"> + <param name="show_log" value="true" /> + </section> + <output name="anndata_out" file="chrY_norm_peaks.h5ad" ftype="h5ad" compare="sim_size"/> + </test> </tests> <help> .. class:: infomark
--- a/macros.xml Tue Apr 18 13:19:11 2023 +0000 +++ b/macros.xml Sat Apr 22 12:14:00 2023 +0000 @@ -1,6 +1,6 @@ <macros> <token name="@TOOL_VERSION@">0.3.2</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> <token name="@PROFILE@">21.01</token> <xml name="requirements"> <requirements>