Mercurial > repos > lldelisle > cooler_cload_tabix

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author lldelisle
date Tue, 02 Apr 2024 07:30:20 +0000
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1 <tool id="cooler_cload_tabix" name="cooler_cload_tabix" version="@VERSION@+galaxy1" profile="22.05">
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2 <description> Create a cool file from a tabix-indexed contact file and a list of genomic bins.</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <expand macro="stdio" />
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8 <command detect_errors="exit_code"><![CDATA[
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9 ##set up input files
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10 ln -s '$format_sel.input_pairs' pairs.tabix &&
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11 ln -s '$format_sel.input_pairs.metadata.tabix_index' pairs.tabix.tbi &&
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12 cooler cload tabix --assembly '$assembly'
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13 #if $format_sel.format == "juicer_medium":
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14 -c2 7 -p2 8
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15 #else:
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16 -c2 $format_sel.c2 -p2 $format_sel.p2
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17 #end if
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18 '$input_bed' pairs.tabix '$output'
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19 ]]>
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20 </command>
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21 <inputs>
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22 <conditional name="format_sel">
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23 <param name="format" type="select" label="Format of your input file">
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24 <option value="juicer_medium">Juicer Medium Format</option>
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25 <option value="other">Other</option>
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26 </param>
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27 <when value="juicer_medium">
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28 <param name="input_pairs" multiple="false" type="data" format="juicer_medium_tabix.gz" label="Select the output of csort_tabix."/>
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29 </when>
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30 <when value="other">
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31 <param name="input_pairs" multiple="false" type="data" format="interval_tabix.gz" label="Select the output of csort_tabix."/>
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32 <param name="c2" type="integer" value="3" label="field number in the input file (starting from 1) of the chromosome of mate 2 (same as in csort).">
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33 <validator type="in_range" min="1" />
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34 </param>
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35 <param name="p2" type="integer" value="4" label="field number in the input file (starting from 1) of the position of mate 2 (same as in csort).">
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36 <validator type="in_range" min="1" />
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37 </param>
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38 </when>
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39 </conditional>
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40 <param name="assembly" type="text" label="name of genome assembly"/>
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41 <param name="input_bed" multiple="false" type="data" format="bed" label="Select the output of makebins."/>
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42 </inputs>
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43
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44 <outputs>
1
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45 <data format="cool" name="output" label="cool file from $format_sel.input_pairs.name and $input_bed.name"/>
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46 </outputs>
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47
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48 <tests>
1
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49 <test>
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50 <conditional name="format_sel">
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51 <param name="format" value="juicer_medium"/>
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52 <param name="input_pairs" value="input.validPairs.tabix" ftype="juicer_medium_tabix.gz"/>
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53 </conditional>
0
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54 <param name="input_bed" value="chr19.1M.bins"/>
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55 <param name="assembly" value="chr19"/>
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56 <output name="output" file="input.cool" compare="sim_size"/>
1
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57 </test>
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58 <test>
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59 <conditional name="format_sel">
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60 <param name="format" value="other"/>
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61 <param name="input_pairs" value="input.validPairs.tabix" ftype="juicer_medium_tabix.gz"/>
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62 <param name="c2" value="7"/>
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63 <param name="p2" value="8"/>
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64 </conditional>
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65 <param name="input_bed" value="chr19.1M.bins"/>
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66 <param name="assembly" value="chr19"/>
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67 <output name="output" file="input.cool" compare="sim_size"/>
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68 </test>
0
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69 </tests>
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70
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71 <help>
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72 **cooler cload**
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73 tool developped by mirnylab
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74 see https://github.com/open2c/cooler
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75 and https://cooler.readthedocs.io/en/latest/cli.html#cooler-cload-tabix
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76
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77 command-line::
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78
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79 cooler cload tabix --assembly assembly -c2 c2 -p2 p2 input_bed input_pairs output
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80
8745321ccc3e planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
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81 </help>
8745321ccc3e planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
lldelisle
parents:
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82 <expand macro="citation_cooler" />
8745321ccc3e planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
lldelisle
parents:
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83 </tool>