Mercurial > repos > lldelisle > cooler_cload_tabix

annotate cooler_cload_tabix.xml @ 0:8745321ccc3e draft

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planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
author lldelisle
date Mon, 24 Oct 2022 15:19:04 +0000
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8745321ccc3e planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
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1 <tool id="cooler_cload_tabix" name="cooler_cload_tabix" version="@VERSION@+galaxy0" profile="18.01">
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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 '$input_pairs' pairs.tabix &&
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11 #if str( $input_pairs.metadata.tabix_index ) != "None":
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12 ln -s '$input_pairs.metadata.tabix_index' pairs.tabix.tbi &&
8745321ccc3e planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit 67c1d2510db398d4f942bb59aca520fdf9cbe296
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13 #else:
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14 tabix -s $pairs_advanced.c1 -b $pairs_advanced.p1 -e $pairs_advanced.p1 pairs.tabix &&
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15 #end if
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16 cooler cload tabix --assembly '$assembly' -c2 $c2 -p2 $p2 '$input_bed' pairs.tabix '$output'
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17 ]]>
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18 </command>
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19 <inputs>
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20 <param name="input_pairs" multiple="false" type="data" format="bgzip,tabix" label="Select the output of csort_tabix."/>
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21 <section name="pairs_advanced" title="If your input is not already indexed" expanded="False">
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22 <param name="c1" type="integer" value="1" label="field number in the input file (starting from 1) of the chromosome of mate 1.">
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23 <validator type="in_range" min="1" />
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24 </param>
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25 <param name="p1" type="integer" value="2" label="field number in the input file (starting from 1) of the position of mate 1.">
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26 <validator type="in_range" min="1" />
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27 </param>
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28 </section>
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29 <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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30 <validator type="in_range" min="1" />
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31 </param>
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32 <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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33 <validator type="in_range" min="1" />
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34 </param>
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35 <param name="assembly" type="text" label="name of genome assembly"/>
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36 <param name="input_bed" multiple="false" type="data" format="bed" label="Select the output of makebins."/>
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37 </inputs>
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38
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39 <outputs>
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40 <data format="cool" name="output" label="cool file from $input_pairs.name and $input_bed.name"/>
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41 </outputs>
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42
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43 <tests>
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44 <!-- For the moment I cannot test this tool -->
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45 <!-- <test>
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46 <param name="input_pairs" value="input.validPairs.tabix" ftype="bgzip"/>
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47 <param name="input_bed" value="chr19.1M.bins"/>
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48 <param name="assembly" value="chr19"/>
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49 <section name="pairs_advanced">
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50 <param name="c1" value="3"/>
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51 <param name="p1" value="4"/>
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52 </section>
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53 <param name="c2" value="7"/>
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54 <param name="p2" value="8"/>
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55 <output name="output" file="input.cool" compare="sim_size"/>
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56 </test> -->
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57 </tests>
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58
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59 <help>
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60 **cooler cload**
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61 tool developped by mirnylab
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62 see https://github.com/open2c/cooler
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63 and https://cooler.readthedocs.io/en/latest/cli.html#cooler-cload-tabix
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64
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65 command-line::
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66
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67 cooler cload tabix --assembly assembly -c2 c2 -p2 p2 input_bed input_pairs output
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68
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69 </help>
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70 <expand macro="citation_cooler" />
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71 </tool>