| Previous changeset 32:4f7a5ccd2ae9 (2018-12-11) Next changeset 34:dde39ba9c031 (2019-04-29) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0a8cabcc8f00014789b6d30e90be1b949d4e94d2 |
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modified:
maskFastaBed.xml test-data/nucBed1.fasta |
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added:
test-data/maskFastaBed_result1.fasta test-data/maskFastaBed_result2.fasta test-data/maskFastaBed_result3.fasta |
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removed:
test-data/maskFastaBed_result1.bed test-data/maskFastaBed_result2.bed |
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| diff -r 4f7a5ccd2ae9 -r 87ee588b3d45 maskFastaBed.xml --- a/maskFastaBed.xml Tue Dec 11 14:01:26 2018 -0500 +++ b/maskFastaBed.xml Mon Dec 17 14:23:31 2018 -0500 |
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| @@ -25,7 +25,7 @@ <param name="mc" type="text" value="N" label="Replace masking character" help="That is, instead of masking with Ns, use another character. (-mc)" /> - <param argument="-fullheader" type="boolean" truevalue="-fullheader" falsevalue="" + <param argument="-fullHeader" name="fullheader" type="boolean" truevalue="-fullHeader" falsevalue="" label="Use full fasta header." help="By default, only the word before the first space or tab is used"/> </inputs> @@ -37,13 +37,20 @@ <param name="input" value="nucBed1.bed" ftype="bed" /> <param name="fasta" value="nucBed1.fasta" ftype="fasta" /> <param name="soft" value="False" /> - <output name="output" file="maskFastaBed_result1.bed" ftype="fasta" /> + <output name="output" file="maskFastaBed_result1.fasta" ftype="fasta" /> </test> <test> <param name="input" value="nucBed1.bed" ftype="bed" /> <param name="fasta" value="nucBed1.fasta" ftype="fasta" /> <param name="soft" value="True" /> - <output name="output" file="maskFastaBed_result2.bed" ftype="fasta" /> + <output name="output" file="maskFastaBed_result2.fasta" ftype="fasta" /> + </test> + <test> + <param name="input" value="nucBed1.bed" ftype="bed" /> + <param name="fasta" value="nucBed1.fasta" ftype="fasta" /> + <param name="soft" value="True" /> + <param name="fullheader" value="True" /> + <output name="output" file="maskFastaBed_result3.fasta" ftype="fasta" /> </test> </tests> <help> |
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| diff -r 4f7a5ccd2ae9 -r 87ee588b3d45 test-data/maskFastaBed_result1.bed --- a/test-data/maskFastaBed_result1.bed Tue Dec 11 14:01:26 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,6 +0,0 @@ ->chr1 -GACTCATGATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN -NNNNNNNNNNNNNNNNNNNNAAACAAGTACCAACCAGAACGTGAAAAAGCGTCCTGCGTGTAGCGTTTATGTTGGTTTCA -TGGTTTTGTCTAACTTTATCGCTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAG -TGGACTGCTGGCGTTATAACGCCGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCA -CCTGTGGCCTGTTGATTCTAAAGGTTAGTTTCTTCACGC |
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| diff -r 4f7a5ccd2ae9 -r 87ee588b3d45 test-data/maskFastaBed_result1.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/maskFastaBed_result1.fasta Mon Dec 17 14:23:31 2018 -0500 |
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| @@ -0,0 +1,6 @@ +>chr1 +GACTCATGATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +NNNNNNNNNNNNNNNNNNNNAAACAAGTACCAACCAGAACGTGAAAAAGCGTCCTGCGTGTAGCGTTTATGTTGGTTTCA +TGGTTTTGTCTAACTTTATCGCTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAG +TGGACTGCTGGCGTTATAACGCCGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCA +CCTGTGGCCTGTTGATTCTAAAGGTTAGTTTCTTCACGC |
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| diff -r 4f7a5ccd2ae9 -r 87ee588b3d45 test-data/maskFastaBed_result2.bed --- a/test-data/maskFastaBed_result2.bed Tue Dec 11 14:01:26 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,6 +0,0 @@ ->chr1 -GACTCATGATttcttacctattagtggttgaacatcgtgatatgtatgttgacggccataaggctgcttcttgttgtcga -tagaacttcatgtgcctgtaAAACAAGTACCAACCAGAACGTGAAAAAGCGTCCTGCGTGTAGCGTTTATGTTGGTTTCA -TGGTTTTGTCTAACTTTATCGCTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAG -TGGACTGCTGGCGTTATAACGCCGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCA -CCTGTGGCCTGTTGATTCTAAAGGTTAGTTTCTTCACGC |
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| diff -r 4f7a5ccd2ae9 -r 87ee588b3d45 test-data/maskFastaBed_result2.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/maskFastaBed_result2.fasta Mon Dec 17 14:23:31 2018 -0500 |
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| @@ -0,0 +1,6 @@ +>chr1 +GACTCATGATttcttacctattagtggttgaacatcgtgatatgtatgttgacggccataaggctgcttcttgttgtcga +tagaacttcatgtgcctgtaAAACAAGTACCAACCAGAACGTGAAAAAGCGTCCTGCGTGTAGCGTTTATGTTGGTTTCA +TGGTTTTGTCTAACTTTATCGCTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAG +TGGACTGCTGGCGTTATAACGCCGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCA +CCTGTGGCCTGTTGATTCTAAAGGTTAGTTTCTTCACGC |
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| diff -r 4f7a5ccd2ae9 -r 87ee588b3d45 test-data/maskFastaBed_result3.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/maskFastaBed_result3.fasta Mon Dec 17 14:23:31 2018 -0500 |
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| @@ -0,0 +1,6 @@ +>chr1 description +GACTCATGATttcttacctattagtggttgaacatcgtgatatgtatgttgacggccataaggctgcttcttgttgtcga +tagaacttcatgtgcctgtaAAACAAGTACCAACCAGAACGTGAAAAAGCGTCCTGCGTGTAGCGTTTATGTTGGTTTCA +TGGTTTTGTCTAACTTTATCGCTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAG +TGGACTGCTGGCGTTATAACGCCGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCA +CCTGTGGCCTGTTGATTCTAAAGGTTAGTTTCTTCACGC |
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| diff -r 4f7a5ccd2ae9 -r 87ee588b3d45 test-data/nucBed1.fasta --- a/test-data/nucBed1.fasta Tue Dec 11 14:01:26 2018 -0500 +++ b/test-data/nucBed1.fasta Mon Dec 17 14:23:31 2018 -0500 |
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| @@ -1,4 +1,4 @@ ->chr1 +>chr1 description GACTCATGATTTCTTACCTATTAGTGGTTGAACATCGTGATATGTATGTTGACGGCCATAAGGCTGCTTCTTGTTGTCGA TAGAACTTCATGTGCCTGTAAAACAAGTACCAACCAGAACGTGAAAAAGCGTCCTGCGTGTAGCGTTTATGTTGGTTTCA TGGTTTTGTCTAACTTTATCGCTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAG |