Mercurial > repos > fubar2 > abslen_bed
changeset 0:551c076a635c draft
Initial upload
| author | fubar2 |
|---|---|
| date | Tue, 05 Dec 2023 10:34:39 +0000 |
| parents | |
| children | aff6409d16d1 |
| files | abslen_bed/.shed.yml abslen_bed/abslen_bed.python.txt abslen_bed/abslen_bed.xml abslen_bed/test-data/absin_sample abslen_bed/test-data/absout_sample |
| diffstat | 5 files changed, 172 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/abslen_bed/.shed.yml Tue Dec 05 10:34:39 2023 +0000 @@ -0,0 +1,6 @@ +category: ToolFactory generated Tools +description: ToolFactory autogenerated tool +name: abslen_bed +owner: fubar2 +synopsis: Add the contig length to the end of each row of a bed file +type: unrestricted
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/abslen_bed/abslen_bed.python.txt Tue Dec 05 10:34:39 2023 +0000 @@ -0,0 +1,14 @@ +#raw +import sys +inp = [] +for line in sys.stdin: + if line.strip() > '': + ls = line.split() + if len(ls) > 3: + x = abs(int(ls[2]) - int(ls[1])) + ls.append((str(x))) + inp.append('\t'.join(ls)) + else: + break +sys.stdout.write('\n'.join(inp)) +#end raw
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/abslen_bed/abslen_bed.xml Tue Dec 05 10:34:39 2023 +0000 @@ -0,0 +1,54 @@ +<tool name="abslen_bed" id="abslen_bed" version="1" profile="22.05"> + <!--Source in git at: https://github.com/fubar2/galaxy_tf_overlay--> + <!--Created by toolfactory@galaxy.org at 05/12/2023 10:23:28 using the Galaxy Tool Factory.--> + <description>Add the contig length to the end of each row of a bed file</description> + <requirements> + <requirement type="package">python</requirement> + </requirements> + <version_command><![CDATA[echo "1"]]></version_command> + <command><![CDATA[python +'$runme' +< +$absin +> +$absout]]></command> + <configfiles> + <configfile name="runme"><![CDATA[#raw +import sys +inp = [] +for line in sys.stdin: + if line.strip() > '': + ls = line.split() + if len(ls) > 3: + x = abs(int(ls[2]) - int(ls[1])) + ls.append((str(x))) + inp.append('\t'.join(ls)) + else: + break +sys.stdout.write('\n'.join(inp)) +#end raw]]></configfile> + </configfiles> + <inputs> + <param name="absin" type="data" optional="false" label="absin" help="Input file to be converted using abs()" format="bed" multiple="false"/> + </inputs> + <outputs> + <data name="absout" format="bed" hidden="false"/> + </outputs> + <tests> + <test> + <param name="absin" value="absin_sample"/> + <output name="absout" value="absout_sample"/> + </test> + </tests> + <help><![CDATA[ + Takes absolute values of the differences between the start and end coordinate of each contig in a bed file. + This tool is a temporary step to enable the Sanger TreeVal NF gap_finder workflow to be + translated into Galaxy. Used after seqtk-cutn to make a tabix file of gaps for an assembly. + + See https://github.com/fubar2/treeval_gal/tree/main/gap_finder + ]]></help> + <citations> + <citation type="doi">10.1093/bioinformatics/bts573</citation> + </citations> +</tool> +
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/abslen_bed/test-data/absout_sample Tue Dec 05 10:34:39 2023 +0000 @@ -0,0 +1,49 @@ +chr1 147962192 147962580 region_0 0 - 388 +chr1 147984545 147984630 region_1 0 + 85 +chr1 148078400 148078582 region_2 0 - 182 +chr1 148185136 148185276 region_3 0 + 140 +chr10 55251623 55253124 region_4 0 - 1501 +chr11 116124407 116124501 region_5 0 - 94 +chr11 116206508 116206563 region_6 0 + 55 +chr11 116211733 116212337 region_7 0 - 604 +chr12 38440094 38440321 region_8 0 - 227 +chr13 112381694 112381953 region_9 0 + 259 +chr14 98710240 98712285 region_10 0 - 2045 +chr15 41486872 41487060 region_11 0 - 188 +chr15 41673708 41673857 region_12 0 + 149 +chr15 41679161 41679250 region_13 0 - 89 +chr16 142908 143003 region_14 0 + 95 +chr16 244413 244681 region_15 0 + 268 +chr16 259268 259383 region_16 0 - 115 +chr18 23786114 23786321 region_17 0 - 207 +chr18 59406881 59407046 region_18 0 + 165 +chr18 59455932 59456337 region_19 0 - 405 +chr19 59068595 59069564 region_20 0 + 969 +chr19 59236026 59236146 region_21 0 - 120 +chr19 59297998 59298008 region_22 0 + 10 +chr2 118288583 118288668 region_23 0 + 85 +chr2 220229609 220230869 region_24 0 - 1260 +chr20 33330413 33330423 region_25 0 - 10 +chr20 33513606 33513792 region_26 0 + 186 +chr21 32869641 32870022 region_27 0 - 381 +chr21 33321040 33322012 region_28 0 + 972 +chr22 30120223 30120265 region_29 0 + 42 +chr22 30160419 30160661 region_30 0 - 242 +chr5 131424298 131424460 region_31 0 + 162 +chr5 131556601 131556672 region_32 0 - 71 +chr5 131621326 131621419 region_33 0 + 93 +chr6 108299600 108299744 region_34 0 - 144 +chr6 108594662 108594687 region_35 0 + 25 +chr6 108640045 108640151 region_36 0 - 106 +chr6 108722976 108723115 region_37 0 + 139 +chr7 113660517 113660685 region_38 0 + 168 +chr7 116512159 116512389 region_39 0 - 230 +chr7 116714099 116714152 region_40 0 + 53 +chr7 116945541 116945787 region_41 0 - 246 +chr8 118881131 118881317 region_42 0 - 186 +chr9 128764156 128764189 region_43 0 + 33 +chr9 128787519 128789136 region_44 0 - 1617 +chrX 122745047 122745924 region_45 0 + 877 +chrX 152648964 152649196 region_46 0 - 232 +chrX 152691446 152691471 region_47 0 + 25 +chrX 152694029 152694263 region_48 0 - 234 \ No newline at end of file