Mercurial > repos > yhoogstrate > crossmap
changeset 11:a5eb1023fc34 draft
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 0acafcc4ce1261ec93eee1ad209a05246f4f02fd-dirty
| author | yhoogstrate |
|---|---|
| date | Wed, 05 Aug 2015 03:53:14 -0400 |
| parents | 4f280582a2fc |
| children | e83cdc4e56cd |
| files | crossmap.xml test-data/aToB.over.chain test-data/test_bed_01_input_a.bed test-data/test_bed_01_output_a__all.bed test-data/test_bed_01_output_a__only-matches.bed test-data/test_bed_02_input_a.bed test-data/test_bed_02_output_a__all.bed test-data/test_bed_02_output_a__only-matches.bed tool_dependencies.xml |
| diffstat | 8 files changed, 592 insertions(+), 19 deletions(-) [+] |
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--- a/crossmap.xml Wed Aug 05 03:11:38 2015 -0400 +++ b/crossmap.xml Wed Aug 05 03:53:14 2015 -0400 @@ -6,7 +6,7 @@ </requirements> <stdio> - <regex match="Usage: CrossMap.py" source="stdin" level="fatal"/> + <regex match="Usage: CrossMap.py" source="stdout" level="fatal"/> <regex match=".*" source="both" level="log" description="tool progress"/> </stdio> @@ -35,10 +35,11 @@ "$multiple.seq_source.input_fasta" #end if - <!-- BED format does not write to the output file, but does write fails to stdout --> - > "$output" + #if $multiple.include_fails == "true" + > + #end if - 2>/dev/null + "$output" </command> <inputs> @@ -73,7 +74,7 @@ </when> <when value="history"> <param type="data" format="bam,sam" name="input" label="BAM/SAM file" /> - <param type="data" name="input_chain" label="LiftOver chain file" /> + <param type="data" format="csv" name="input_chain" label="LiftOver chain file" /> </when> </conditional> @@ -105,9 +106,10 @@ </when> <when value="history"> <param type="data" format="bed" name="input" label="BED file" help="BED format file must have at least 3 columns (chrom, start, end) and no more than 12 columns." /> - <param type="data" name="input_chain" label="LiftOver chain file" /> + <param type="data" format="csv" name="input_chain" label="LiftOver chain file" /> </when> </conditional> + <param name="include_fails" type="boolean" truevalue="true" falsevalue="false" label="Include failed liftovers" help="If a coordinate can not be lift over, do you want to include it in the output (it is still being marked 'fail')" /> </when> <when value="bigwig"> <conditional name="seq_source"> @@ -130,8 +132,8 @@ </param> </when> <when value="history"> - <param format="bigwig" name="input" type="data" label="BigWig file" /> - <param type="data" name="input_chain" label="LiftOver chain file" /> + <param type="data" format="bigwig" name="input" label="BigWig file" /> + <param type="data" format="csv" name="input_chain" label="LiftOver chain file" /> </when> </conditional> </when> @@ -156,8 +158,8 @@ </param> </when> <when value="history"> - <param format="gtf,gff,gff3" name="input" type="data" label="GTF/GFF file" /> - <param type="data" name="input_chain" label="LiftOver chain file" /> + <param type="data" format="gtf,gff,gff3" name="input" label="GTF/GFF file" /> + <param type="data" format="csv" name="input_chain" label="LiftOver chain file" /> </when> </conditional> </when> @@ -199,7 +201,7 @@ <validator type="unspecified_build" /> <validator type="dataset_metadata_in_file" filename="all_fasta.loc" metadata_name="dbkey" metadata_column="1" message="LiftOver mapping (FASTA file) is not available for the specified build." /> </param> - <param type="data" name="input_chain" multiple="false" label="LiftOver chain file" /> + <param type="data" format="csv" name="input_chain" multiple="false" label="LiftOver chain file" /> <param name="input_fasta" type="select" label="Lift Over To (FASTA file)" help="The FASTA file must be on the same build (dbkey) as the LiftOver chain file"> <options from_file="all_fasta.loc"> <column name="name" index="2"/> @@ -211,8 +213,8 @@ <when value="history_all"> <param type="data" format="vcf" name="input" label="VCF file" /> - <param type="data" name="input_all_chain" multiple="false" label="LiftOver chain file" /> - <param type="data" format="fasta" name="input_all_fasta" multiple="false" label="Full genome FASTA file" /> + <param type="data" format="csv" name="input_chain" multiple="false" label="LiftOver chain file" /> + <param type="data" format="fasta" name="input_fasta" multiple="false" label="Full genome FASTA file" /> </when> </conditional> </when> @@ -238,7 +240,7 @@ </when> <when value="history"> <param format="wig" name="input" type="data" label="Wiggle file" /> - <param type="data" name="input_chain" label="LiftOver chain file" /> + <param type="data" format="csv" name="input_chain" label="LiftOver chain file" /> </when> </conditional> </when> @@ -251,10 +253,41 @@ <tests> <test> - <param name="input" value="test1.hg19.txt"/> - <param name="input" value="hg18tohg19.chain"/> - <output name="output" file="test1.hg18.txt"/> + <param name="input_format" value="bed"/> + <param name="index_source" value="history"/> + <param name="input" value="test_bed_01_input_a.bed" ftype="bed"/> + <param name="input_chain" value="aToB.over.chain" ftype="txt"/> + <param name="include_fails" value="false"/> + + <output name="output" file="test_bed_01_output_a__only-matches.bed"/> + </test> + <!--<test> + <param name="input_format" value="bed"/> + <param name="index_source" value="history"/> + <param name="input" value="test_bed_01_input_a.bed" ftype="bed"/> + <param name="input_chain" value="aToB.over.chain" ftype="txt"/> + <param name="include_fails" value="true"/> + + <output name="output" file="test_bed_02_output_a__all.bed"/> </test> + <test> + <param name="input_format" value="bed"/> + <param name="index_source" value="history"/> + <param name="input" value="test_bed_02_input_a.bed" ftype="bed"/> + <param name="input_chain" value="aToB.over.chain" ftype="txt"/> + <param name="include_fails" value="false"/> + + <output name="output" file="test_bed_02_output_a__only-matches.bed"/> + </test> + <test> + <param name="input_format" value="bed"/> + <param name="index_source" value="history"/> + <param name="input" value="test_bed_02_input_a.bed" ftype="bed"/> + <param name="input_chain" value="aToB.over.chain" ftype="txt"/> + <param name="include_fails" value="true"/> + + <output name="output" file="test_bed_02_output_a__all.bed"/> + </test>--> </tests> <help> @@ -267,7 +300,6 @@ ------------ BED format file must have at least 3 columns (chrom, start, end) and no more than 12 columns. BED format: http://genome.ucsc.edu/FAQ/FAQformat.html#format1 - </help> <citations>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/aToB.over.chain Wed Aug 05 03:53:14 2015 -0400 @@ -0,0 +1,498 @@ +chain 21270171362 chr1 249250621 + 10000 249233096 chr1 247249719 + 0 247199719 2 +619 137 0 +166661 50000 50000 +40302 50000 50000 +153649 50000 50000 +1098479 1 1 +47 1 1 +73 117 114 +773 1 1 +43 1 1 +864369 2 2 +51 3 0 +104 13694 13694 +104 0 3 +51 2 2 +134936 50000 50000 +1161048 150000 60000 +1440092 27273 50000 +7590365 50000 50000 +116914 100000 50000 +237250 50000 50000 +3518496 50000 50000 +12702424 150000 50000 +16145012 0 1 +7772 1 0 +4705841 0 1 +52977198 50000 50000 +157344 21065 50000 +16604841 50000 50000 +189539 150000 50000 +398739 21050000 20290000 +195588 50000 50000 +186739 150000 50000 +175055 50000 50000 +201709 100000 50000 +126477 130183 50000 +381 0 3 +315 0 2 +62 1 1 +45 1 0 +19 0 1 +8 1 1 +1158 1 0 +314 12 13 +2849 3 0 +5615 1 1 +37 1 1 +3172 6 4 +190 1 1 +34 1 1 +380 0 1 +2099 3 0 +765 2 2 +366 0 4 +1186 1 0 +460 0 1 +1242 28 28 +574 1 1 +21 1 1 +1460 1 1 +105 1 1 +701 3 0 +239 0 1 +970 11 11 +2365 1 1 +21 1 1 +384 8 8 +996 2 0 +10383 2 0 +713 0 1 +5188 1 1 +30 1 1 +1233 1 0 +132 1 1 +44 1 1 +1123 22 22 +1810 1 0 +512 1 1 +39 1 1 +1096 0 16 +743 1 0 +9028 0 1 +2506 0 6 +8446 2 0 +5505 0 3 +7541 1 0 +109864 50000 50000 +78698 50000 50000 +127263 50000 50000 +170669 50000 50000 +38311 100000 100000 +1022394 50000 50000 +281532 289973 50000 +1648 1539 0 +76 3225 3 +1018 34 34 +1716 2 0 +159 4 0 +1600 0 6 +1385 1 0 +2066 1 1 +32 1 3 +1556908 150000 50000 +185320 150000 50000 +172789 50000 50000 +220313 50000 50000 +455185 50000 50000 +22047237 1 0 +34365824 150000 50000 +259514 150000 50000 +17265625 50000 50000 +11394365 50000 50000 +13665999 150000 50000 +174886 + +chain 22466185064 chr2 243199373 + 10000 243102476 chr2 242951149 + 0 242751149 1 +1201236 0 1 +2057 1 1 +26 1 1 +4043 22 0 +82 7 101 +33 84 0 +26 1 23 +67 48 0 +176 318 0 +40 92 0 +33 0 74 +62 0 6 +22 0 118 +387 2446 0 +843 2450 0 +167 2304 0 +21342 1 1 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2 +108126 0 145 +3542 1 0 +10276 0 1 +402 1 1 +47 1 1 +63 2 0 +583 1 1 +34 1 1 +8974 0 46 +379 1 1 +70 1 1 +2474 0 102 +1756 0 1 +8426 0 1 +11986570 151150 142000 +14207 1 1 +49 1 1 +1781 0 12 +409 1 0 +1874 1 1 +33 1 1 +4795 2 0 +3686 1 1 +15 1 1 +164 2 0 +7287 5 5 +702023 72796 150000 +69 1 0 +1598 0 1 +1340 0 1 +1030 0 4 +1166 10 10 +6406 1 1 +34 1 1 +3283 2 4 +496 1 23 +25 10 0 +40 1 1 +21282 2 1 +1406 0 44 +937 17 0 +18255 1 0 +172366 0 281526 +40517 0 406 +58864 1 2 +1843 0 2 +14994 0 1 +12992 2 0 +2571146 1 0 +35688061 108224 100000 +29671719 1 0 +39665349 1 0 +14876089 64197 20000 +401 0 3 +1831 1 1 +61 1 1 +654 11 1 +127 0 28 +116 25 29 +74 9 9 +3247 2 0 +1355 1 0 +816 1 0 +21 3 0 +526 1 1 +60 1 1 +773 1 0 +1494 1 0 +1683 1 0 +21 1 1 +596 1 0 +1582 1 0 +425 0 3 +1139 0 8 +138 144 813 +71 1 0 +385638 1 1 +219 1 1 +51 7 7 +54 15205 15205 +54 7 7 +51 1 1 +110 1 1 +5198249 0 1 +115 80 0 +60 40 0 +80 100 20 +442 1 1 +35 1 1 +119 9 129 +14 0 40 +61 1 1 +85 0 40 +1331 0 1 +1194 12 14 +1773 0 5 +1623 1 1 +25 1 1 +2422 21 22 +2315 0 1 +31 1 1 +1508 0 3 +50 0 4 +970 6 6 +7234 4 0 +1228 1 0 +1233 8 1 +4207 1 1 +41 1 1 +1715 50 50 +1532 0 2 +1714 2 0 +2299 2 0 +2143 1 1 +18 1 1 +917 1 0 +1082 1 1 +49 1 1 +9098 0 4 +5529 0 1 +3266 0 8 +894 6 0 +1440 1 1 +2095 2 0 +4179 18 13 +1785 0 1 +1674 0 6 +1217 32348 33000 +287 17 23 +40 173 0 +20 161 0 +13 66 0 +12 71 1 +12548 30000 30000 +952154 41011 25000 +1914 1 0 +225 1 1 +57 1 1 +2910 0 1 +471 1 0 +1956 1 1 +43 1 1 +991 0 92 +2863 3 0 +1838 306 0 +1006 30 0 +206 1 1 +27 0 3 +221 17 17 +1525 8 0 +413 1 1 +32 2 2 +1573 12 12 +2258676 + +chain 18404394637 chr3 198022430 + 60000 197962430 chr3 199501827 + 35000 199446827 3 +13552792 0 1 +585083 0 1 +2092 1 2 +71 0 1 +31067262 0 1 +90 1 0 +5628461 0 15 +788 1 0 +3676 0 2 +35 1 1 +4682 1 0 +1295 0 5 +437 53 42 +326 0 2 +3309 1 1 +40 1 1 +998 0 3 +3584 5 0 +930 5 7 +845 1 1 +28 2 1 +303 0 1 +507 0 5 +5088 1 0 +2185 10046 10048 +949 4 4 +35 1 1 +2874 0 1 +6717 0 1 +2823 1 0 +703 0 4 +5143 1 0 +2490 10 10 +162 7 7 +6308 0 15 +15177535 152352 260003 +2532 1 0 +1633 2 2 +24207544 3000000 4400000 +60453436 0 4 +40076813 20999 20000 +8195 1 1 +44 1 1 +1408 1 1 +33 1 1 +172 3 4 +25 1 1 +538 13 13 +173 1 1 +27 1 1 +636 1 1 +28 1 1 +470 3 3 +112 1 1 +375 1 1 +26 26 0 +115 78 0 +52 23 0 +104 26 0 +15 231 0 +56 1 1 +20 1 1 +815 16 16 +484 1 1 +49 18 0 +509 4 3 +23 1 1 +391 1 1 +44 1 1 +1278 0 4 +32 1 1 +263 4 0 +27 1 1 +2416 0 2 +3184 43 43 +1150 13 13 +736 1 1 +47 1 1 +1416 1 1 +20 1 1 +1020 1 1 +25 1 1 +482 5 0 +716 1 0 +1697 1 1 +29 1 1 +1270261 23108 27000 +40930 1 0 +17455 1 1 +28 4 4 +43 0 491 +1679 1 1 +33 7 5 +29 1 3 +54863 53 16 +7653 2 2 +29 2 2 +15 0 30 +180 0 75 +215 45 0 +360 915 0 +6188 96 0 +17 288 0 +1388 1 1 +37 1 1 +7956 0 1 +374 0 1 +2442058 + +chain 310844 chr4 191154276 + 9241835 9252105 chr4 191273063 + 8941714 8947231 850 +2726 14 14 +243 9 9 +78 4 4 +157 213 211 +265 85 85 +524 4751 0 +379 283 283 +539 + +chain 9105 chr4 191154276 + 8982741 8983189 chr10 135374737 - 120304868 120305301 22041837 +59 380 365 +9
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_bed_01_input_a.bed Wed Aug 05 03:53:14 2015 -0400 @@ -0,0 +1,5 @@ +chr1 100000 1000000 +chr2 100000 1000000 +chr3 100000 1000000 +chr4 9200000 9250000 +chr4 8940000 9000000
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_bed_01_output_a__all.bed Wed Aug 05 03:53:14 2015 -0400 @@ -0,0 +1,14 @@ +chr1 100000 1000000 (split.1:chr1:100000:177417:+) chr1 89863 167280 +chr1 100000 1000000 (split.2:chr1:227417:267719:+) chr1 217280 257582 +chr1 100000 1000000 (split.3:chr1:317719:471368:+) chr1 307582 461231 +chr1 100000 1000000 (split.4:chr1:521368:1000000:+) chr1 511231 989863 +chr2 100000 1000000 -> chr2 90000 990000 +chr3 100000 1000000 -> chr3 75000 975000 +chr4 9200000 9250000 (split.1:chr4:9241835:9244561:+) chr4 8941714 8944440 +chr4 9200000 9250000 (split.2:chr4:9244575:9244818:+) chr4 8944454 8944697 +chr4 9200000 9250000 (split.3:chr4:9244827:9244905:+) chr4 8944706 8944784 +chr4 9200000 9250000 (split.4:chr4:9244909:9245066:+) chr4 8944788 8944945 +chr4 9200000 9250000 (split.5:chr4:9245279:9245544:+) chr4 8945156 8945421 +chr4 9200000 9250000 (split.6:chr4:9245629:9246153:+) chr4 8945506 8946030 +chr4 8940000 9000000 (split.1:chr4:8982741:8982800:+) chr10 15069810 15069869 +chr4 8940000 9000000 (split.2:chr4:8983180:8983189:+) chr10 15069436 15069445
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_bed_01_output_a__only-matches.bed Wed Aug 05 03:53:14 2015 -0400 @@ -0,0 +1,14 @@ +chr1 89863 167280 +chr1 217280 257582 +chr1 307582 461231 +chr1 511231 989863 +chr2 90000 990000 +chr3 75000 975000 +chr4 8941714 8944440 +chr4 8944454 8944697 +chr4 8944706 8944784 +chr4 8944788 8944945 +chr4 8945156 8945421 +chr4 8945506 8946030 +chr10 15069810 15069869 +chr10 15069436 15069445
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_bed_02_input_a.bed Wed Aug 05 03:53:14 2015 -0400 @@ -0,0 +1,5 @@ +chr1 100 10000 +chr2 100 10000 +chr3 100 10000 +chr4 8941700 8947200 +chr5 1 100000000 \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_bed_02_output_a__all.bed Wed Aug 05 03:53:14 2015 -0400 @@ -0,0 +1,5 @@ +chr1 100 10000 Fail +chr2 100 10000 Fail +chr3 100 10000 Fail +chr4 8941700 8947200 Fail +chr5 1 100000000 Fail
--- a/tool_dependencies.xml Wed Aug 05 03:11:38 2015 -0400 +++ b/tool_dependencies.xml Wed Aug 05 03:53:14 2015 -0400 @@ -1,6 +1,6 @@ <?xml version="1.0"?> <tool_dependency> <package name="crossmap" version="0.1.9"> - <repository changeset_revision="d427ce441805" name="package_crossmap_0_1_9" owner="yhoogstrate" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="7c9668f97b2e" name="package_crossmap_0_1_9" owner="yhoogstrate" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> </tool_dependency>