Mercurial > repos > lldelisle > cooler_cload_tabix
comparison cooler_cload_tabix.xml @ 1:3ff6eeca667e draft
planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit f7ba0eeedb7768690962c0538df0507110605f43
| author | lldelisle |
|---|---|
| date | Thu, 01 Dec 2022 11:21:36 +0000 |
| parents | 8745321ccc3e |
| children |
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| 0:8745321ccc3e | 1:3ff6eeca667e |
|---|---|
| 1 <tool id="cooler_cload_tabix" name="cooler_cload_tabix" version="@VERSION@+galaxy0" profile="18.01"> | 1 <tool id="cooler_cload_tabix" name="cooler_cload_tabix" version="@VERSION@+galaxy1" profile="22.05"> |
| 2 <description> Create a cool file from a tabix-indexed contact file and a list of genomic bins.</description> | 2 <description> Create a cool file from a tabix-indexed contact file and a list of genomic bins.</description> |
| 3 <macros> | 3 <macros> |
| 4 <import>macros.xml</import> | 4 <import>macros.xml</import> |
| 5 </macros> | 5 </macros> |
| 6 <expand macro="requirements" /> | 6 <expand macro="requirements" /> |
| 7 <expand macro="stdio" /> | 7 <expand macro="stdio" /> |
| 8 <command detect_errors="exit_code"><![CDATA[ | 8 <command detect_errors="exit_code"><![CDATA[ |
| 9 ##set up input files | 9 ##set up input files |
| 10 ln -s '$input_pairs' pairs.tabix && | 10 ln -s '$format_sel.input_pairs' pairs.tabix && |
| 11 #if str( $input_pairs.metadata.tabix_index ) != "None": | 11 ln -s '$format_sel.input_pairs.metadata.tabix_index' pairs.tabix.tbi && |
| 12 ln -s '$input_pairs.metadata.tabix_index' pairs.tabix.tbi && | 12 cooler cload tabix --assembly '$assembly' |
| 13 #if $format_sel.format == "juicer_medium": | |
| 14 -c2 7 -p2 8 | |
| 13 #else: | 15 #else: |
| 14 tabix -s $pairs_advanced.c1 -b $pairs_advanced.p1 -e $pairs_advanced.p1 pairs.tabix && | 16 -c2 $format_sel.c2 -p2 $format_sel.p2 |
| 15 #end if | 17 #end if |
| 16 cooler cload tabix --assembly '$assembly' -c2 $c2 -p2 $p2 '$input_bed' pairs.tabix '$output' | 18 '$input_bed' pairs.tabix '$output' |
| 17 ]]> | 19 ]]> |
| 18 </command> | 20 </command> |
| 19 <inputs> | 21 <inputs> |
| 20 <param name="input_pairs" multiple="false" type="data" format="bgzip,tabix" label="Select the output of csort_tabix."/> | 22 <conditional name="format_sel"> |
| 21 <section name="pairs_advanced" title="If your input is not already indexed" expanded="False"> | 23 <param name="format" type="select" label="Format of your input file"> |
| 22 <param name="c1" type="integer" value="1" label="field number in the input file (starting from 1) of the chromosome of mate 1."> | 24 <option value="juicer_medium">Juicer Medium Format</option> |
| 23 <validator type="in_range" min="1" /> | 25 <option value="other">Other</option> |
| 24 </param> | 26 </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."> | 27 <when value="juicer_medium"> |
| 26 <validator type="in_range" min="1" /> | 28 <param name="input_pairs" multiple="false" type="data" format="juicer_medium_tabix.gz" label="Select the output of csort_tabix."/> |
| 27 </param> | 29 </when> |
| 28 </section> | 30 <when value="other"> |
| 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)."> | 31 <param name="input_pairs" multiple="false" type="data" format="interval_tabix.gz" label="Select the output of csort_tabix."/> |
| 30 <validator type="in_range" min="1" /> | 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)."> |
| 31 </param> | 33 <validator type="in_range" min="1" /> |
| 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)."> | 34 </param> |
| 33 <validator type="in_range" min="1" /> | 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)."> |
| 34 </param> | 36 <validator type="in_range" min="1" /> |
| 37 </param> | |
| 38 </when> | |
| 39 </conditional> | |
| 35 <param name="assembly" type="text" label="name of genome assembly"/> | 40 <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."/> | 41 <param name="input_bed" multiple="false" type="data" format="bed" label="Select the output of makebins."/> |
| 37 </inputs> | 42 </inputs> |
| 38 | 43 |
| 39 <outputs> | 44 <outputs> |
| 40 <data format="cool" name="output" label="cool file from $input_pairs.name and $input_bed.name"/> | 45 <data format="cool" name="output" label="cool file from $format_sel.input_pairs.name and $input_bed.name"/> |
| 41 </outputs> | 46 </outputs> |
| 42 | 47 |
| 43 <tests> | 48 <tests> |
| 44 <!-- For the moment I cannot test this tool --> | 49 <test> |
| 45 <!-- <test> | 50 <conditional name="format_sel"> |
| 46 <param name="input_pairs" value="input.validPairs.tabix" ftype="bgzip"/> | 51 <param name="format" value="juicer_medium"/> |
| 52 <param name="input_pairs" value="input.validPairs.tabix" ftype="juicer_medium_tabix.gz"/> | |
| 53 </conditional> | |
| 47 <param name="input_bed" value="chr19.1M.bins"/> | 54 <param name="input_bed" value="chr19.1M.bins"/> |
| 48 <param name="assembly" value="chr19"/> | 55 <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 <output name="output" file="input.cool" compare="sim_size"/> |
| 56 </test> --> | 57 </test> |
| 58 <test> | |
| 59 <conditional name="format_sel"> | |
| 60 <param name="format" value="other"/> | |
| 61 <param name="input_pairs" value="input.validPairs.tabix" ftype="juicer_medium_tabix.gz"/> | |
| 62 <param name="c2" value="7"/> | |
| 63 <param name="p2" value="8"/> | |
| 64 </conditional> | |
| 65 <param name="input_bed" value="chr19.1M.bins"/> | |
| 66 <param name="assembly" value="chr19"/> | |
| 67 <output name="output" file="input.cool" compare="sim_size"/> | |
| 68 </test> | |
| 57 </tests> | 69 </tests> |
| 58 | 70 |
| 59 <help> | 71 <help> |
| 60 **cooler cload** | 72 **cooler cload** |
| 61 tool developped by mirnylab | 73 tool developped by mirnylab |