Mercurial > repos > iuc > episcanpy_build_matrix

annotate build_matrix.xml @ 0:eb4f81df2159 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
author iuc
date Tue, 18 Apr 2023 13:18:07 +0000
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children 0004aee8b905
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eb4f81df2159 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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1 <tool id="episcanpy_build_matrix" name="Build count matrix" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
eb4f81df2159 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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2 <description>with EpiScanpy</description>
eb4f81df2159 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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3 <macros>
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4 <import>macros.xml</import>
eb4f81df2159 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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5 </macros>
eb4f81df2159 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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6 <expand macro="bio_tools"/>
eb4f81df2159 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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7 <expand macro="requirements"/>
eb4f81df2159 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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8 <expand macro="version_command"/>
eb4f81df2159 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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9 <command detect_errors="exit_code"><![CDATA[
eb4f81df2159 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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10 bgzip -c '$fragment_file' > fragments.gz &&
eb4f81df2159 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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11 tabix -p bed fragments.gz &&
eb4f81df2159 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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12 cat '$script_file' > '$hidden_output' &&
eb4f81df2159 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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13 python '$script_file' >> '$hidden_output' &&
eb4f81df2159 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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14 touch 'anndata_info.txt' &&
eb4f81df2159 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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15 cat 'anndata_info.txt' @CMD_prettify_stdout@
eb4f81df2159 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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16 ]]></command>
eb4f81df2159 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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17 <configfiles>
eb4f81df2159 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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18 <configfile name="script_file"><![CDATA[
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19 @CMD_imports@
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20 peaks = esc.ct.load_peaks('$peaks_file')
eb4f81df2159 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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21 esc.ct.norm_peaks(peaks, extension=$extension)
eb4f81df2159 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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22 esc.ct.bld_mtx_bed(
eb4f81df2159 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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23 fragment_file='fragments.gz',
eb4f81df2159 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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24 feature_region=peaks,
eb4f81df2159 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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25 #if $reference_chr.chr_select == 'custom'
eb4f81df2159 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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26 #set $chromosomes = ([x.strip() for x in str($reference_chr.chromosomes).split(',')])
eb4f81df2159 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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27 chromosomes=$chromosomes,
eb4f81df2159 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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28 #else
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29 chromosomes='$reference_chr.chr_select',
eb4f81df2159 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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30 #end if
eb4f81df2159 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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31 save='anndata.h5ad')
eb4f81df2159 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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32 ]]></configfile>
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33 </configfiles>
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34 <inputs>
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35 <param name="fragment_file" type="data" format="bed" label="ATAC fragments file" />
eb4f81df2159 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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36 <param name="peaks_file" type="data" format="tabular" label="Features file" help="Peaks BED file or MACS2 narrowPeak file"/>
eb4f81df2159 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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37 <param name="extension" type="integer" value="0" min="0" label="Number of bases to extend both sides of peaks" />
eb4f81df2159 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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38 <conditional name="reference_chr">
eb4f81df2159 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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39 <param name="chr_select" type="select" label="Select the chromosomes of the species you are considering" >
eb4f81df2159 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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40 <option value="human">Human chromosomes ['1', '2', '3', ... , '22', 'X', 'Y']</option>
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41 <option value="mouse">Mouse chromosomes ['1', '2', '3', ... ', '19', 'X', 'Y']</option>
eb4f81df2159 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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42 <option value="custom">Custom list of chromosomes</option>
eb4f81df2159 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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43 </param>
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44 <when value="human" />
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45 <when value="mouse" />
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46 <when value="custom">
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47 <param name="chromosomes" value="" type="text" label="Enter comma seperated list of chromosome ids (without chr prefix)" >
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48 <expand macro="sanitize_query" />
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49 </param>
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50 </when>
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51 </conditional>
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52 <expand macro="inputs_common_advanced"/>
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53 </inputs>
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54 <outputs>
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55 <data name="anndata_out" format="h5ad" from_work_dir="anndata.h5ad" label="${tool.name} on ${on_string}: Annotated data matrix"/>
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56 <data name="hidden_output" format="txt" label="Log file" hidden="true" >
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57 <filter>advanced_common['show_log']</filter>
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58 </data>
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59 </outputs>
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60 <tests>
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61 <test expect_num_outputs="2">
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62 <!-- count matrix -->
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63 <param name="fragment_file" value="chrY.fragments.bed" />
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64 <param name="peaks_file" value="chrY.peaks.bed" />
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65 <conditional name="reference_chr">
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66 <param name="chr_select" value="custom" />
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67 <param name="chromosomes" value="Y" />
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68 </conditional>
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69 <section name="advanced_common">
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70 <param name="show_log" value="true" />
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71 </section>
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72 <output name="anndata_out" file="chrY.h5ad" ftype="h5ad" compare="sim_size"/>
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73 </test>
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74 </tests>
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75 <help>
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76 .. class:: infomark
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77
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78 **What it does**
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79
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80 Builds single-cell ATAC-seq count matrix in Anndata format.
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81
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82 -----
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83
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84 **Inputs**
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85
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86 - ATAC fragments containing the positions of Tn5 integration sites, the cell barcode that the DNA fragment originated from, and the number of times the fragment was sequenced. An example::
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87
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88 chrY 2650256 2650533 GACCAATGTCCGTAGC 1
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89 chrY 2650420 2650463 TGACAACGTACTTCAG 1
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90 chrY 2650444 2650643 GTGGATTGTACAAGCG 3
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91 chrY 2650639 2650990 ATAGGCTAGGGCTCTC 2
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92 chrY 2650650 2650692 GACTAACAGCAACGGT 1
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93 chrY 2650699 2650942 TCAAAGCTCAAAGTAG 1
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94 chrY 2650768 2650809 TTGTTGTAGGGCATTG 2
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95 chrY 2650841 2650873 TTGTTGTAGGGCATTG 1
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96 chrY 2650957 2650995 GACTAACAGCAACGGT 1
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97 chrY 2651205 2651265 TCAAAGCTCAAAGTAG 1
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98 chrY 2651215 2651268 TCACAAGGTCAAGACG 1
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99
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100 - Features file. A plain BED file with peak locations or narrowPeak file from MACS2.
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101
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102 **Output**
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103
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104 - Count matrix in Anndata format.
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105
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106 </help>
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107 <expand macro="citations"/>
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108 </tool>