| Next changeset 1:201c568972c3 (2016-03-11) |
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Commit message:
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda |
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added:
catWrapper.xml test-data/1.bed test-data/2.bed test-data/cat_wrapper_out1.bed |
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| diff -r 000000000000 -r 1e06fa2771f9 catWrapper.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/catWrapper.xml Fri Sep 25 11:09:17 2015 -0400 |
| [ |
| @@ -0,0 +1,70 @@ +<tool id="cat_multiple" name="Concatenate multiple datasets" version="0.2"> + <description>tail-to-head</description> + <command><![CDATA[ + cat + #for $file in $input + "$file" + #end for + > "$out_file1" + ]]> + </command> + <inputs> + <param name="input" type="data" label="Concatenate Dataset" multiple="True"/> + </inputs> + <outputs> + <data name="out_file1" format_source="input" metadata_source="input"/> + </outputs> + <tests> + <test> + <param name="input" value="1.bed,2.bed"/> + <output name="out_file1" file="cat_wrapper_out1.bed"/> + </test> + </tests> + <help> + + .. class:: warningmark + + **WARNING:** Be careful not to concatenate datasets of different kinds (e.g., sequences with intervals). This + tool does not check if the datasets being concatenated are in the same format. + + ----- + + **What it does** + + Concatenates datasets + + ----- + + **Example** + + Concatenating Dataset:: + + chrX 151087187 151087355 A 0 - + chrX 151572400 151572481 B 0 + + + with Dataset1:: + + chr1 151242630 151242955 X 0 + + chr1 151271715 151271999 Y 0 + + chr1 151278832 151279227 Z 0 - + + and with Dataset2:: + + chr2 100000030 200000955 P 0 + + chr2 100000015 200000999 Q 0 + + + will result in the following:: + + chrX 151087187 151087355 A 0 - + chrX 151572400 151572481 B 0 + + chr1 151242630 151242955 X 0 + + chr1 151271715 151271999 Y 0 + + chr1 151278832 151279227 Z 0 - + chr2 100000030 200000955 P 0 + + chr2 100000015 200000999 Q 0 + + + ----- + + Adapted from the concatenate tool that comes with galaxy. + </help> +</tool> |
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| diff -r 000000000000 -r 1e06fa2771f9 test-data/1.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/1.bed Fri Sep 25 11:09:17 2015 -0400 |
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| @@ -0,0 +1,65 @@ +chr1 147962192 147962580 CCDS989.1_cds_0_0_chr1_147962193_r 0 - +chr1 147984545 147984630 CCDS990.1_cds_0_0_chr1_147984546_f 0 + +chr1 148078400 148078582 CCDS993.1_cds_0_0_chr1_148078401_r 0 - +chr1 148185136 148185276 CCDS996.1_cds_0_0_chr1_148185137_f 0 + +chr10 55251623 55253124 CCDS7248.1_cds_0_0_chr10_55251624_r 0 - +chr11 116124407 116124501 CCDS8374.1_cds_0_0_chr11_116124408_r 0 - +chr11 116206508 116206563 CCDS8377.1_cds_0_0_chr11_116206509_f 0 + +chr11 116211733 116212337 CCDS8378.1_cds_0_0_chr11_116211734_r 0 - +chr11 1812377 1812407 CCDS7726.1_cds_0_0_chr11_1812378_f 0 + +chr12 38440094 38440321 CCDS8736.1_cds_0_0_chr12_38440095_r 0 - +chr13 112381694 112381953 CCDS9526.1_cds_0_0_chr13_112381695_f 0 + +chr14 98710240 98712285 CCDS9949.1_cds_0_0_chr14_98710241_r 0 - +chr15 41486872 41487060 CCDS10096.1_cds_0_0_chr15_41486873_r 0 - +chr15 41673708 41673857 CCDS10097.1_cds_0_0_chr15_41673709_f 0 + +chr15 41679161 41679250 CCDS10098.1_cds_0_0_chr15_41679162_r 0 - +chr15 41826029 41826196 CCDS10101.1_cds_0_0_chr15_41826030_f 0 + +chr16 142908 143003 CCDS10397.1_cds_0_0_chr16_142909_f 0 + +chr16 179963 180135 CCDS10401.1_cds_0_0_chr16_179964_r 0 - +chr16 244413 244681 CCDS10402.1_cds_0_0_chr16_244414_f 0 + +chr16 259268 259383 CCDS10403.1_cds_0_0_chr16_259269_r 0 - +chr18 23786114 23786321 CCDS11891.1_cds_0_0_chr18_23786115_r 0 - +chr18 59406881 59407046 CCDS11985.1_cds_0_0_chr18_59406882_f 0 + +chr18 59455932 59456337 CCDS11986.1_cds_0_0_chr18_59455933_r 0 - +chr18 59600586 59600754 CCDS11988.1_cds_0_0_chr18_59600587_f 0 + +chr19 59068595 59069564 CCDS12866.1_cds_0_0_chr19_59068596_f 0 + +chr19 59236026 59236146 CCDS12872.1_cds_0_0_chr19_59236027_r 0 - +chr19 59297998 59298008 CCDS12877.1_cds_0_0_chr19_59297999_f 0 + +chr19 59302168 59302288 CCDS12878.1_cds_0_0_chr19_59302169_r 0 - +chr2 118288583 118288668 CCDS2120.1_cds_0_0_chr2_118288584_f 0 + +chr2 118394148 118394202 CCDS2121.1_cds_0_0_chr2_118394149_r 0 - +chr2 220190202 220190242 CCDS2441.1_cds_0_0_chr2_220190203_f 0 + +chr2 220229609 220230869 CCDS2443.1_cds_0_0_chr2_220229610_r 0 - +chr20 33330413 33330423 CCDS13249.1_cds_0_0_chr20_33330414_r 0 - +chr20 33513606 33513792 CCDS13255.1_cds_0_0_chr20_33513607_f 0 + +chr20 33579500 33579527 CCDS13256.1_cds_0_0_chr20_33579501_r 0 - +chr20 33593260 33593348 CCDS13257.1_cds_0_0_chr20_33593261_f 0 + +chr21 32707032 32707192 CCDS13614.1_cds_0_0_chr21_32707033_f 0 + +chr21 32869641 32870022 CCDS13615.1_cds_0_0_chr21_32869642_r 0 - +chr21 33321040 33322012 CCDS13620.1_cds_0_0_chr21_33321041_f 0 + +chr21 33744994 33745040 CCDS13625.1_cds_0_0_chr21_33744995_r 0 - +chr22 30120223 30120265 CCDS13897.1_cds_0_0_chr22_30120224_f 0 + +chr22 30160419 30160661 CCDS13898.1_cds_0_0_chr22_30160420_r 0 - +chr22 30665273 30665360 CCDS13901.1_cds_0_0_chr22_30665274_f 0 + +chr22 30939054 30939266 CCDS13903.1_cds_0_0_chr22_30939055_r 0 - +chr5 131424298 131424460 CCDS4149.1_cds_0_0_chr5_131424299_f 0 + +chr5 131556601 131556672 CCDS4151.1_cds_0_0_chr5_131556602_r 0 - +chr5 131621326 131621419 CCDS4152.1_cds_0_0_chr5_131621327_f 0 + +chr5 131847541 131847666 CCDS4155.1_cds_0_0_chr5_131847542_r 0 - +chr6 108299600 108299744 CCDS5061.1_cds_0_0_chr6_108299601_r 0 - +chr6 108594662 108594687 CCDS5063.1_cds_0_0_chr6_108594663_f 0 + +chr6 108640045 108640151 CCDS5064.1_cds_0_0_chr6_108640046_r 0 - +chr6 108722976 108723115 CCDS5067.1_cds_0_0_chr6_108722977_f 0 + +chr7 113660517 113660685 CCDS5760.1_cds_0_0_chr7_113660518_f 0 + +chr7 116512159 116512389 CCDS5771.1_cds_0_0_chr7_116512160_r 0 - +chr7 116714099 116714152 CCDS5773.1_cds_0_0_chr7_116714100_f 0 + +chr7 116945541 116945787 CCDS5774.1_cds_0_0_chr7_116945542_r 0 - +chr8 118881131 118881317 CCDS6324.1_cds_0_0_chr8_118881132_r 0 - +chr9 128764156 128764189 CCDS6914.1_cds_0_0_chr9_128764157_f 0 + +chr9 128787519 128789136 CCDS6915.1_cds_0_0_chr9_128787520_r 0 - +chr9 128882427 128882523 CCDS6917.1_cds_0_0_chr9_128882428_f 0 + +chr9 128937229 128937445 CCDS6919.1_cds_0_0_chr9_128937230_r 0 - +chrX 122745047 122745924 CCDS14606.1_cds_0_0_chrX_122745048_f 0 + +chrX 152648964 152649196 CCDS14733.1_cds_0_0_chrX_152648965_r 0 - +chrX 152691446 152691471 CCDS14735.1_cds_0_0_chrX_152691447_f 0 + +chrX 152694029 152694263 CCDS14736.1_cds_0_0_chrX_152694030_r 0 - |
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| diff -r 000000000000 -r 1e06fa2771f9 test-data/2.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/2.bed Fri Sep 25 11:09:17 2015 -0400 |
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| @@ -0,0 +1,68 @@ +chr1 147962192 147962580 NM_005997_cds_0_0_chr1_147962193_r 0 - +chr1 147984545 147984630 BC007833_cds_0_0_chr1_147984546_f 0 + +chr1 148078400 148078582 AJ011123_cds_0_0_chr1_148078401_r 0 - +chr1 148185136 148185276 NM_002796_cds_0_0_chr1_148185137_f 0 + +chr10 55251623 55253124 AY029205_cds_0_0_chr10_55251624_r 0 - +chr11 116124407 116124501 AK057832_cds_0_0_chr11_116124408_r 0 - +chr11 116206508 116206563 NM_000040_cds_1_0_chr11_116206509_f 0 + +chr11 116211733 116212337 BC005380_cds_0_0_chr11_116211734_r 0 - +chr11 130745911 130745993 AY358331_cds_0_0_chr11_130745912_f 0 + +chr12 38440094 38440321 NM_052885_cds_0_0_chr12_38440095_r 0 - +chr12 38905200 38905351 AY792511_cds_0_0_chr12_38905201_f 0 + +chr13 112381694 112381953 NM_207440_cds_1_0_chr13_112381695_f 0 + +chr13 29680676 29680875 NM_032116_cds_0_0_chr13_29680677_r 0 - +chr14 98521864 98521922 U88895_cds_0_0_chr14_98521865_f 0 + +chr14 98710240 98712285 NM_022898_cds_0_0_chr14_98710241_r 0 - +chr15 41486872 41487060 BX537418_cds_0_0_chr15_41486873_r 0 - +chr15 41673708 41673857 AK223365_cds_0_0_chr15_41673709_f 0 + +chr15 41679161 41679250 NM_153700_cds_0_0_chr15_41679162_r 0 - +chr15 41773540 41773689 AK223365_cds_0_0_chr15_41773541_f 0 + +chr16 142908 143003 NM_005332_cds_0_0_chr16_142909_f 0 + +chr16 179197 179339 BC065198_cds_0_0_chr16_179198_r 0 - +chr16 244413 244681 AK057165_cds_2_0_chr16_244414_f 0 + +chr16 259268 259383 AB016929_cds_0_0_chr16_259269_r 0 - +chr18 23786114 23786321 NM_001792_cds_0_0_chr18_23786115_r 0 - +chr18 59406881 59407046 NM_012397_cds_1_0_chr18_59406882_f 0 + +chr18 59455932 59456337 AB046400_cds_0_0_chr18_59455933_r 0 - +chr18 59528407 59528575 AY792326_cds_0_0_chr18_59528408_f 0 + +chr19 59068595 59069564 BC013995_cds_1_0_chr19_59068596_f 0 + +chr19 59236026 59236146 NM_198481_cds_0_0_chr19_59236027_r 0 - +chr19 59297998 59298008 NM_004542_cds_0_0_chr19_59297999_f 0 + +chr19 59318205 59318718 AK128544_cds_3_0_chr19_59318206_r 0 - +chr2 118288583 118288668 NM_006773_cds_0_0_chr2_118288584_f 0 + +chr2 118390395 118390500 BC005078_cds_0_0_chr2_118390396_r 0 - +chr2 220108689 220109267 AY125465_cds_0_0_chr2_220108690_f 0 + +chr2 220229609 220230869 NM_024536_cds_0_0_chr2_220229610_r 0 - +chr20 33330413 33330423 NM_181466_cds_0_0_chr20_33330414_r 0 - +chr20 33485370 33486123 BC085019_cds_1_0_chr20_33485371_f 0 + +chr20 33488491 33489122 NM_000557_cds_1_0_chr20_33488492_r 0 - +chr20 33513606 33513792 AF022655_cds_1_0_chr20_33513607_f 0 + +chr21 32687402 32687588 NM_032910_cds_0_0_chr21_32687403_f 0 + +chr21 32869641 32870022 NM_018277_cds_3_0_chr21_32869642_r 0 - +chr21 33321040 33322012 NM_005806_cds_1_0_chr21_33321041_f 0 + +chr21 33728358 33728724 AK129657_cds_0_0_chr21_33728359_r 0 - +chr22 30120223 30120265 NM_004147_cds_0_0_chr22_30120224_f 0 + +chr22 30160419 30160661 BC032941_cds_0_0_chr22_30160420_r 0 - +chr22 30228824 30228916 NM_001007467_cds_1_0_chr22_30228825_f 0 + +chr22 30340151 30340376 CR456540_cds_0_0_chr22_30340152_r 0 - +chr5 131311206 131311254 AF099740_cds_11_0_chr5_131311207_r 0 - +chr5 131424298 131424460 NM_000588_cds_0_0_chr5_131424299_f 0 + +chr5 131556601 131556672 BC035813_cds_0_0_chr5_131556602_r 0 - +chr5 131621326 131621419 BC003096_cds_0_0_chr5_131621327_f 0 + +chr6 108299600 108299744 NM_007214_cds_0_0_chr6_108299601_r 0 - +chr6 108594662 108594687 NM_003269_cds_0_0_chr6_108594663_f 0 + +chr6 108640045 108640151 NM_003795_cds_0_0_chr6_108640046_r 0 - +chr6 108722976 108723115 NM_145315_cds_0_0_chr6_108722977_f 0 + +chr7 113660517 113660685 AF467257_cds_1_0_chr7_113660518_f 0 + +chr7 116512159 116512389 NM_003391_cds_0_0_chr7_116512160_r 0 - +chr7 116714099 116714152 NM_000492_cds_0_0_chr7_116714100_f 0 + +chr7 116945541 116945787 AF377960_cds_0_0_chr7_116945542_r 0 - +chr8 118881131 118881317 NM_000127_cds_0_0_chr8_118881132_r 0 - +chr9 128764156 128764189 BC051300_cds_0_0_chr9_128764157_f 0 + +chr9 128787519 128789136 NM_014908_cds_0_0_chr9_128787520_r 0 - +chr9 128789552 128789584 NM_015354_cds_0_0_chr9_128789553_f 0 + +chr9 128850516 128850624 AB058751_cds_0_0_chr9_128850517_r 0 - +chrX 122745047 122745924 NM_001167_cds_1_0_chrX_122745048_f 0 + +chrX 152648964 152649196 NM_000425_cds_0_0_chrX_152648965_r 0 - +chrX 152691446 152691471 AF101728_cds_0_0_chrX_152691447_f 0 + +chrX 152694029 152694263 BC052303_cds_0_0_chrX_152694030_r 0 - |
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| diff -r 000000000000 -r 1e06fa2771f9 test-data/cat_wrapper_out1.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cat_wrapper_out1.bed Fri Sep 25 11:09:17 2015 -0400 |
| b |
| b'@@ -0,0 +1,133 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022898_cds_0_0_chr14_98710241_r\t0\t-\n+chr15\t41486872\t41487060\tBX537418_cds_0_0_chr15_41486873_r\t0\t-\n+chr15\t41673708\t41673857\tAK223365_cds_0_0_chr15_41673709_f\t0\t+\n+chr15\t41679161\t41679250\tNM_153700_cds_0_0_chr15_41679162_r\t0\t-\n+chr15\t41773540\t41773689\tAK223365_cds_0_0_chr15_41773541_f\t0\t+\n+chr16\t142908\t143003\tNM_005332_cds_0_0_chr16_142909_f\t0\t+\n+chr16\t179197\t179339\tBC065198_cds_0_0_chr16_179198_r\t0\t-\n+chr16\t244413\t244681\tAK057165_cds_2_0_chr16_244414_f\t0\t+\n+chr16\t259268\t259383\tAB016929_cds_0_0_chr16_259269_r\t0\t-\n+chr18\t23786114\t23786321\tNM_001792_cds_0_0_chr18_23786115_r\t0\t-\n+chr18\t59406881\t59407046\tNM_012397_cds_1_0_chr18_59406882_f\t0\t+\n+chr18\t59455932\t59456337\tAB046400_cds_0_0_chr18_59455933_r\t0\t-\n+chr18\t59528407\t59528575\tAY792326_cds_0_0_chr18_59528408_f\t0\t+\n+chr19\t59068595\t59069564\tBC013995_cds_1_0_chr19_59068596_f\t0\t+\n+chr19\t59236026\t59236146\tNM_198481_cds_0_0_chr19_59236027_r\t0\t-\n+chr19\t59297998\t59298008\tNM_004542_cds_0_0_chr19_59297999_f\t0\t+\n+chr19\t59318205\t59318718\tAK128544_cds_3_0_chr19_59318206_r\t0\t-\n+chr2\t118288583\t118288668\tNM_006773_cds_0_0_chr2_118288584_f\t0\t+\n+chr2\t118390395\t118390500\tBC005078_cds_0_0_chr2_118390396_r\t0\t-\n+chr2\t220108689\t220109267\tAY125465_cds_0_0_chr2_220108690_f\t0\t+\n+chr2\t220229609\t220230869\tNM_024536_cds_0_0_chr2_220229610_r\t0\t-\n+chr20\t33330413\t33330423\tNM_181466_cds_0_0_chr20_33330414_r\t0\t-\n+chr20\t33485370\t33486123\tBC085019_cds_1_0_chr20_33485371_f\t0\t+\n+chr20\t33488491\t33489122\tNM_000557_cds_1_0_chr20_33488492_r\t0\t-\n+chr20\t33513606\t33513792\tAF022655_cds_1_0_chr20_33513607_f\t0\t+\n+chr21\t32687402\t32687588\tNM_032910_cds_0_0_chr21_32687403_f\t0\t+\n+chr21\t32869641\t32870022\tNM_018277_cds_3_0_chr21_32869642_r\t0\t-\n+chr21\t33321040\t33322012\tNM_005806_cds_1_0_chr21_33321041_f\t0\t+\n+chr21\t33728358\t33728724\tAK129657_cds_0_0_chr21_33728359_r\t0\t-\n+chr22\t30120223\t30120265\tNM_004147_cds_0_0_chr22_30120224_f\t0\t+\n+chr22\t30160419\t30160661\tBC032941_cds_0_0_chr22_30160420_r\t0\t-\n+chr22\t30228824\t30228916\tNM_001007467_cds_1_0_chr22_30228825_f\t0\t+\n+chr22\t30340151\t30340376\tCR456540_cds_0_0_chr22_30340152_r\t0\t-\n+chr5\t131311206\t131311254\tAF099740_cds_11_0_chr5_131311207_r\t0\t-\n+chr5\t131424298\t131424460\tNM_000588_cds_0_0_chr5_131424299_f\t0\t+\n+chr5\t131556601\t131556672\tBC035813_cds_0_0_chr5_131556602_r\t0\t-\n+chr5\t131621326\t131621419\tBC003096_cds_0_0_chr5_131621327_f\t0\t+\n+chr6\t108299600\t108299744\tNM_007214_cds_0_0_chr6_108299601_r\t0\t-\n+chr6\t108594662\t108594687\tNM_003269_cds_0_0_chr6_108594663_f\t0\t+\n+chr6\t108640045\t108640151\tNM_003795_cds_0_0_chr6_108640046_r\t0\t-\n+chr6\t108722976\t108723115\tNM_145315_cds_0_0_chr6_108722977_f\t0\t+\n+chr7\t113660517\t113660685\tAF467257_cds_1_0_chr7_113660518_f\t0\t+\n+chr7\t116512159\t116512389\tNM_003391_cds_0_0_chr7_116512160_r\t0\t-\n+chr7\t116714099\t116714152\tNM_000492_cds_0_0_chr7_116714100_f\t0\t+\n+chr7\t116945541\t116945787\tAF377960_cds_0_0_chr7_116945542_r\t0\t-\n+chr8\t118881131\t118881317\tNM_000127_cds_0_0_chr8_118881132_r\t0\t-\n+chr9\t128764156\t128764189\tBC051300_cds_0_0_chr9_128764157_f\t0\t+\n+chr9\t128787519\t128789136\tNM_014908_cds_0_0_chr9_128787520_r\t0\t-\n+chr9\t128789552\t128789584\tNM_015354_cds_0_0_chr9_128789553_f\t0\t+\n+chr9\t128850516\t128850624\tAB058751_cds_0_0_chr9_128850517_r\t0\t-\n+chrX\t122745047\t122745924\tNM_001167_cds_1_0_chrX_122745048_f\t0\t+\n+chrX\t152648964\t152649196\tNM_000425_cds_0_0_chrX_152648965_r\t0\t-\n+chrX\t152691446\t152691471\tAF101728_cds_0_0_chrX_152691447_f\t0\t+\n+chrX\t152694029\t152694263\tBC052303_cds_0_0_chrX_152694030_r\t0\t-\n' |