Mercurial > repos > iuc > episcanpy_build_matrix
annotate build_matrix.xml @ 0:1bf008d6d54e draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
author | iuc |
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date | Tue, 18 Apr 2023 13:19:11 +0000 |
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children | 31a21ba2c5ea |
rev | line source |
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0
1bf008d6d54e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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1 <tool id="episcanpy_build_matrix" name="Build count matrix" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> |
1bf008d6d54e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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2 <description>with EpiScanpy</description> |
1bf008d6d54e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
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3 <macros> |
1bf008d6d54e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
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4 <import>macros.xml</import> |
1bf008d6d54e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
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changeset
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5 </macros> |
1bf008d6d54e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
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6 <expand macro="bio_tools"/> |
1bf008d6d54e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
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7 <expand macro="requirements"/> |
1bf008d6d54e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff
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8 <expand macro="version_command"/> |
1bf008d6d54e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
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9 <command detect_errors="exit_code"><![CDATA[ |
1bf008d6d54e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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10 bgzip -c '$fragment_file' > fragments.gz && |
1bf008d6d54e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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11 tabix -p bed fragments.gz && |
1bf008d6d54e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
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12 cat '$script_file' > '$hidden_output' && |
1bf008d6d54e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
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13 python '$script_file' >> '$hidden_output' && |
1bf008d6d54e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
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14 touch 'anndata_info.txt' && |
1bf008d6d54e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
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15 cat 'anndata_info.txt' @CMD_prettify_stdout@ |
1bf008d6d54e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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16 ]]></command> |
1bf008d6d54e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
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17 <configfiles> |
1bf008d6d54e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
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18 <configfile name="script_file"><![CDATA[ |
1bf008d6d54e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
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19 @CMD_imports@ |
1bf008d6d54e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
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20 peaks = esc.ct.load_peaks('$peaks_file') |
1bf008d6d54e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
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21 esc.ct.norm_peaks(peaks, extension=$extension) |
1bf008d6d54e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
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22 esc.ct.bld_mtx_bed( |
1bf008d6d54e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
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23 fragment_file='fragments.gz', |
1bf008d6d54e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
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24 feature_region=peaks, |
1bf008d6d54e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
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25 #if $reference_chr.chr_select == 'custom' |
1bf008d6d54e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
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26 #set $chromosomes = ([x.strip() for x in str($reference_chr.chromosomes).split(',')]) |
1bf008d6d54e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
diff
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27 chromosomes=$chromosomes, |
1bf008d6d54e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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28 #else |
1bf008d6d54e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
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29 chromosomes='$reference_chr.chr_select', |
1bf008d6d54e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
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30 #end if |
1bf008d6d54e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
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31 save='anndata.h5ad') |
1bf008d6d54e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
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32 ]]></configfile> |
1bf008d6d54e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
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33 </configfiles> |
1bf008d6d54e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
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34 <inputs> |
1bf008d6d54e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
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35 <param name="fragment_file" type="data" format="bed" label="ATAC fragments file" /> |
1bf008d6d54e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
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36 <param name="peaks_file" type="data" format="tabular" label="Features file" help="Peaks BED file or MACS2 narrowPeak file"/> |
1bf008d6d54e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
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37 <param name="extension" type="integer" value="0" min="0" label="Number of bases to extend both sides of peaks" /> |
1bf008d6d54e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
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38 <conditional name="reference_chr"> |
1bf008d6d54e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
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39 <param name="chr_select" type="select" label="Select the chromosomes of the species you are considering" > |
1bf008d6d54e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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40 <option value="human">Human chromosomes ['1', '2', '3', ... , '22', 'X', 'Y']</option> |
1bf008d6d54e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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41 <option value="mouse">Mouse chromosomes ['1', '2', '3', ... ', '19', 'X', 'Y']</option> |
1bf008d6d54e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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42 <option value="custom">Custom list of chromosomes</option> |
1bf008d6d54e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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43 </param> |
1bf008d6d54e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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44 <when value="human" /> |
1bf008d6d54e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
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45 <when value="mouse" /> |
1bf008d6d54e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
parents:
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46 <when value="custom"> |
1bf008d6d54e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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47 <param name="chromosomes" value="" type="text" label="Enter comma seperated list of chromosome ids (without chr prefix)" > |
1bf008d6d54e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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48 <expand macro="sanitize_query" /> |
1bf008d6d54e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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49 </param> |
1bf008d6d54e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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50 </when> |
1bf008d6d54e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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51 </conditional> |
1bf008d6d54e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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52 <expand macro="inputs_common_advanced"/> |
1bf008d6d54e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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53 </inputs> |
1bf008d6d54e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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54 <outputs> |
1bf008d6d54e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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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"/> |
1bf008d6d54e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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56 <data name="hidden_output" format="txt" label="Log file" hidden="true" > |
1bf008d6d54e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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57 <filter>advanced_common['show_log']</filter> |
1bf008d6d54e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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58 </data> |
1bf008d6d54e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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59 </outputs> |
1bf008d6d54e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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60 <tests> |
1bf008d6d54e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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61 <test expect_num_outputs="2"> |
1bf008d6d54e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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62 <!-- count matrix --> |
1bf008d6d54e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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63 <param name="fragment_file" value="chrY.fragments.bed" /> |
1bf008d6d54e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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64 <param name="peaks_file" value="chrY.peaks.bed" /> |
1bf008d6d54e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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65 <conditional name="reference_chr"> |
1bf008d6d54e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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66 <param name="chr_select" value="custom" /> |
1bf008d6d54e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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67 <param name="chromosomes" value="Y" /> |
1bf008d6d54e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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68 </conditional> |
1bf008d6d54e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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69 <section name="advanced_common"> |
1bf008d6d54e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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70 <param name="show_log" value="true" /> |
1bf008d6d54e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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71 </section> |
1bf008d6d54e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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72 <output name="anndata_out" file="chrY.h5ad" ftype="h5ad" compare="sim_size"/> |
1bf008d6d54e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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73 </test> |
1bf008d6d54e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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74 </tests> |
1bf008d6d54e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
iuc
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75 <help> |
1bf008d6d54e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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76 .. class:: infomark |
1bf008d6d54e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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77 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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78 **What it does** |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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79 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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80 Builds single-cell ATAC-seq count matrix in Anndata format. |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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81 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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82 ----- |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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83 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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84 **Inputs** |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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85 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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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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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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87 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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88 chrY 2650256 2650533 GACCAATGTCCGTAGC 1 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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89 chrY 2650420 2650463 TGACAACGTACTTCAG 1 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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90 chrY 2650444 2650643 GTGGATTGTACAAGCG 3 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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91 chrY 2650639 2650990 ATAGGCTAGGGCTCTC 2 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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92 chrY 2650650 2650692 GACTAACAGCAACGGT 1 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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93 chrY 2650699 2650942 TCAAAGCTCAAAGTAG 1 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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94 chrY 2650768 2650809 TTGTTGTAGGGCATTG 2 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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95 chrY 2650841 2650873 TTGTTGTAGGGCATTG 1 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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96 chrY 2650957 2650995 GACTAACAGCAACGGT 1 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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97 chrY 2651205 2651265 TCAAAGCTCAAAGTAG 1 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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98 chrY 2651215 2651268 TCACAAGGTCAAGACG 1 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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99 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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100 - Features file. A plain BED file with peak locations or narrowPeak file from MACS2. |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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101 |
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102 **Output** |
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103 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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104 - Count matrix in Anndata format. |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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105 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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106 </help> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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107 <expand macro="citations"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
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108 </tool> |