Mercurial > repos > lldelisle > cooler_cload_tabix
comparison cooler_cload_tabix.xml @ 0:8745321ccc3e draft
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 |
| parents | |
| children | 3ff6eeca667e |
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| -1:000000000000 | 0:8745321ccc3e |
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| 1 <tool id="cooler_cload_tabix" name="cooler_cload_tabix" version="@VERSION@+galaxy0" profile="18.01"> | |
| 2 <description> Create a cool file from a tabix-indexed contact file and a list of genomic bins.</description> | |
| 3 <macros> | |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements" /> | |
| 7 <expand macro="stdio" /> | |
| 8 <command detect_errors="exit_code"><![CDATA[ | |
| 9 ##set up input files | |
| 10 ln -s '$input_pairs' pairs.tabix && | |
| 11 #if str( $input_pairs.metadata.tabix_index ) != "None": | |
| 12 ln -s '$input_pairs.metadata.tabix_index' pairs.tabix.tbi && | |
| 13 #else: | |
| 14 tabix -s $pairs_advanced.c1 -b $pairs_advanced.p1 -e $pairs_advanced.p1 pairs.tabix && | |
| 15 #end if | |
| 16 cooler cload tabix --assembly '$assembly' -c2 $c2 -p2 $p2 '$input_bed' pairs.tabix '$output' | |
| 17 ]]> | |
| 18 </command> | |
| 19 <inputs> | |
| 20 <param name="input_pairs" multiple="false" type="data" format="bgzip,tabix" label="Select the output of csort_tabix."/> | |
| 21 <section name="pairs_advanced" title="If your input is not already indexed" expanded="False"> | |
| 22 <param name="c1" type="integer" value="1" label="field number in the input file (starting from 1) of the chromosome of mate 1."> | |
| 23 <validator type="in_range" min="1" /> | |
| 24 </param> | |
| 25 <param name="p1" type="integer" value="2" label="field number in the input file (starting from 1) of the position of mate 1."> | |
| 26 <validator type="in_range" min="1" /> | |
| 27 </param> | |
| 28 </section> | |
| 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)."> | |
| 30 <validator type="in_range" min="1" /> | |
| 31 </param> | |
| 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)."> | |
| 33 <validator type="in_range" min="1" /> | |
| 34 </param> | |
| 35 <param name="assembly" type="text" label="name of genome assembly"/> | |
| 36 <param name="input_bed" multiple="false" type="data" format="bed" label="Select the output of makebins."/> | |
| 37 </inputs> | |
| 38 | |
| 39 <outputs> | |
| 40 <data format="cool" name="output" label="cool file from $input_pairs.name and $input_bed.name"/> | |
| 41 </outputs> | |
| 42 | |
| 43 <tests> | |
| 44 <!-- For the moment I cannot test this tool --> | |
| 45 <!-- <test> | |
| 46 <param name="input_pairs" value="input.validPairs.tabix" ftype="bgzip"/> | |
| 47 <param name="input_bed" value="chr19.1M.bins"/> | |
| 48 <param name="assembly" value="chr19"/> | |
| 49 <section name="pairs_advanced"> | |
| 50 <param name="c1" value="3"/> | |
| 51 <param name="p1" value="4"/> | |
| 52 </section> | |
| 53 <param name="c2" value="7"/> | |
| 54 <param name="p2" value="8"/> | |
| 55 <output name="output" file="input.cool" compare="sim_size"/> | |
| 56 </test> --> | |
| 57 </tests> | |
| 58 | |
| 59 <help> | |
| 60 **cooler cload** | |
| 61 tool developped by mirnylab | |
| 62 see https://github.com/open2c/cooler | |
| 63 and https://cooler.readthedocs.io/en/latest/cli.html#cooler-cload-tabix | |
| 64 | |
| 65 command-line:: | |
| 66 | |
| 67 cooler cload tabix --assembly assembly -c2 c2 -p2 p2 input_bed input_pairs output | |
| 68 | |
| 69 </help> | |
| 70 <expand macro="citation_cooler" /> | |
| 71 </tool> |