Repository 'sequence_format_converter'
hg clone https://toolshed.g2.bx.psu.edu/repos/artbio/sequence_format_converter

Changeset 4:1c14d2869d4d (2021-03-17)
Previous changeset 3:772bd67ef26a (2020-05-11)
Commit message:
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 9c5f0b8e89dfe4347c610f42923f0acad2ecc81b"
modified:
sequence_format_converter.xml
test-data/output.tab
b
diff -r 772bd67ef26a -r 1c14d2869d4d sequence_format_converter.xml
--- a/sequence_format_converter.xml Mon May 11 19:58:45 2020 -0400
+++ b/sequence_format_converter.xml Wed Mar 17 22:09:13 2021 +0000
[
@@ -1,5 +1,8 @@
-<tool id="sequence_format_converter" name="sequence_format_converter" version="2.1.2">
+<tool id="sequence_format_converter" name="sequence_format_converter" version="2.2.0">
   <description></description>
+    <requirements>
+        <requirement type="package" version="3.7.6">python</requirement>
+    </requirements>
   <command><![CDATA[
     #if $input.is_of_type('fastq.gz'):
       gzip -dc $input > '${input}.tmp';
@@ -38,7 +41,7 @@
             <!-- convertion fasta to tabular -->
             <param name="output_format" value="tabular" />
             <param ftype="fasta" name="input" value="input.fa" />
-            <output file="output.tab" name="output" />
+            <output file="output.tab" name="output" sort="true" />
         </test>
         <test>
             <!-- convertion tabular to fasta -->
b
diff -r 772bd67ef26a -r 1c14d2869d4d test-data/output.tab
--- a/test-data/output.tab Mon May 11 19:58:45 2020 -0400
+++ b/test-data/output.tab Wed Mar 17 22:09:13 2021 +0000
b
b'@@ -1,247 +1,247 @@\n ACAGCAGGACGGTGATCA\t2\n-TGCTTGGACTACATATGGTTGAGTG\t2\n TGGAATGTAAAGAAGTATGGAG\t2\n-AATTTATTTAATTTATATTCTAACTAA\t1\n-TTATAATCACGGCACCCTATACA\t1\n-TCCGAAAAATCGTAGGACCCGGGCA\t1\n-TCCCAACCCTCGAGCATCATTTTC\t1\n-TTGATTCTTCTTTTTCACAAAA\t1\n-AGAACAATTAAATAAAATAGCATA\t1\n-CCAGAAAACAATACAACATCCTCA\t1\n-TCTAGTCTGAGCGTAGTACCAGATTG\t1\n-TTTTTAACTCCCATCATTTTTCCTC\t1\n-GCAGATAGAAATCAATACAAAAATC\t1\n-AAGTGAAGAAGTAGTTTTT\t1\n-AATGTCACTTGAAGAATTCACGT\t1\n-TTTACCAGAGGAGTCGAGTTTTT\t1\n-GGTATCTTTATATTTTAATTTTCTT\t1\n+TGCTTGGACTACATATGGTTGAGTG\t2\n+TAGTTACCTTCATATCTCTCTTTA\t1\n+TCTATTCATACAAAACACTAATACCC\t1\n+ACAACCTCAACTCATATTT\t1\n+TATAATTTTATTTTATATTTTCTCT\t1\n+TCTTCTATATAATCCTTTATTATAA\t1\n+TAAAATAAACCAAAACCCAAAAAT\t1\n+AATCTACAATTTCCATTACGACTCC\t1\n+TTTCCGACAAATACACCATCTTC\t1\n+CAGATTCACTGATTTTCTTACGCC\t1\n+CAAGAATACAAAAAATACTAATTA\t1\n+AACTCTCTAATTTAACTTTGTGC\t1\n+AAAAACACACAGACACAAGCAGCAAT\t1\n TTACTAGATCCACCCTCATTA\t1\n-TATATAAATCTTCAACATCAA\t1\n-GAAACCATTATCTTATCTTTATACA\t1\n-GGAGATTGTAGAACGAAAGGAAAAT\t1\n-ACTAAACTTTTCTTACCATATTTCTA\t1\n-TCAAGCCTTTTGAAGAACTGACCTAAA\t1\n-TAACATAAATTTTAATCATAAATTG\t1\n-TAGCGAGATGGACCAACGTGCTGT\t1\n-TACAAACGTAATTTTCGCATAACATC\t1\n-CGGAAAAGAATGTAGACCATTTAA\t1\n-GAAAGGAAGGGAAGAAAGCGAAAGGA\t1\n-CAAGAATACAAAAAATACTAATTA\t1\n+ATGTTATTTACTTTTTCCCCTTATA\t1\n+CGATATTTTCTCCTCTTACC\t1\n+TACAGAGAAATATACAACACTCACC\t1\n+ATGAAATTCGAACAATACGTC\t1\n+GAGAATAAATATTTCAATGGTCTATTG\t1\n+TGCTTTTACTACATATTTTTTATTTTTTTA\t1\n+CATACCTTAAATTATCTCTTTCTT\t1\n+TTTGTTTTTCATTTTTTTATCTTT\t1\n+TTATTATCTATTTTAATTTTTCTTAA\t1\n+TATTATCATCTCGTTCTTCCTTCTC\t1\n+TCAACTGGCAAGAATTTTTGAAAATT\t1\n+TACAAATTTTTTTTTCTTTCTTAT\t1\n+TTTTCTTTTTTTCATTTTCTCTTTTA\t1\n+AAGATGGAGTAGTTTTTT\t1\n+TCTCATCTTACAATTTTTTAAAACTT\t1\n CATACCTACAAAAAAGCTTCTCTTAC\t1\n-TAAAATAAATAAGTCCGACGACAA\t1\n-AGGAATATGATGAAATAAAAAAAT\t1\n-TTTTTTTTTTGTTTTTATTTTTATCAT\t1\n-TTTTTAACTCATTTTACAATTAAAC\t1\n-CCGCGATCTGCTTATTTATAATCTT\t1\n-TAGGTACTTACCTTTTTTTTACACAA\t1\n-TCATTACACTTCTTACAAAAC\t1\n-TATTATACATAGAATAACAAATCTTT\t1\n-ATGTTATTTACTTTTTCCCCTTATA\t1\n-TCCGAAAACAAGGCCCGTCGCT\t1\n-TGCTTTTACTACATATTTTTTATTTTTTTA\t1\n-GAACAATTTTTCAATTTTTTACATTA\t1\n-AACATTTTATCAATTATACATTA\t1\n-TATCTGATCAACAATCTTTTCCCAT\t1\n-AATTGCAACAGAGACTGGAA\t1\n-TATTCAATCACTCCATTATATATAACA\t1\n-CAAACGGAACAAGACATCACCATC\t1\n-TCTTCTATATAATCCTTTATTATAA\t1\n-TGATGACGGGCAGCAGGGATTTTC\t1\n+TTTTATATTTCCTTATATCTTTACTA\t1\n+GGAGATTGTAGAACGAAAGGAAAAT\t1\n+TCTATTTCTTTATTTTTTTTATTAT\t1\n+CGGACGGTATATTTTTTAATATAA\t1\n+TTCTTGGACTACACATTTTTTATTGTTTTA\t1\n+TACTATATACTTCTTCAAATCACA\t1\n+ATTTTACTTCATCATTTTC\t1\n+TATTTCCAACCTTCAACCTCAAATAA\t1\n+CACGACTTTATTCTTTTTATCTCA\t1\n+TTCTTTTACTACATATTTTTTATTTTTTTA\t1\n TTTATTACAACCCTATCTTACCTCAA\t1\n-AACAGGAAAAACAGAAGGATTTCTA\t1\n CGATATTTTCTCCTCGTACC\t1\n-AAATTGCAAAGATGGAAAATAAAACT\t1\n-TACACACTCATCAACCAAAGGACG\t1\n-TATATTGCCTCCCCATAATCCTT\t1\n-TACAAACGGAACTTTCTTCATAACTTC\t1\n-GGACGGAGAACTGATAATGGC\t1\n-TTCTTTGACTACATATTTTTTATT\t1\n-TCTTTTTTTTAATACTTATTTTCATT\t1\n+TAATTACCATTGCTAACTATCCA\t1\n+CATTAATTCATCCATTTAAACTAA\t1\n+GAAACAAACAACACATACCCTCTGGC\t1\n TACTTTTTTCTTAATTTTTTATTAAAC\t1\n-AATATAAAAATACAATCAACCATTGCA\t1\n+TAACTTTAACTTTTTTACT\t1\n+TTCTTTTACTACATATTGTTTATTTTTTTA\t1\n+TCTAGTCTGAGCGTAGTACCAGATTG\t1\n+TTTTTTATCAATTTTCACCATTCAT\t1\n+AATGACACACTCTTCATCAAC\t1\n+TAACATAAATTTTAATCATAAATTG\t1\n+TCTATATTATTTTTATCAATTTTCACC\t1\n+TCCCAACCCTCGAGCATCATTTTC\t1\n+TAGTCATACATACCTAATTATACATA\t1\n+TACAAAAAATGCGAAAATTGACCCT\t1\n+GAGAACTTTTAATCATTTTAC\t1\n+TCTTATTTTAATCTTCCAATTTC\t1\n+CGGCACATGTTGAATTACACTCA\t1\n CAGTTTCACAAAAGATCTTTTAA\t1\n-GAAACAAACAACACATACCCTCTGGC\t1\n-AATGACACACTCTTCATCAAC\t1\n-AAGATGGAGTAGTTTTTT\t1\n-ACAACCTCAACTCATATTT\t1\n+GCCAACGACCATACCACGA\t1\n+CAAATAACAAACTGAATAAACGAAA\t1\n+TAGTTTCACTACTTTATTCTTTTTA\t1\n+TGAGGAAAACAGAAAAATGAGAGACA\t1\n+TATATAAATCTTCAACATCAA\t1\n+TGATTTACTTACATTCTTTTTTT\t1\n+CTTCTTTTACTACATATTTTTTATTTTTTTA\t1\n+TACTGAAAACGGGCGCATATCAGTGG\t1\n+TATTCAATCACTCCATTATATATAACA\t1\n+TATATTGCCTCCCCATAATCCTT\t1\n+TCGCCGTAAAGCCAGTCGTTCTCC\t1\n+TTTAAACACTTCCTACATCAAATTTC\t1\n+TTTGTTTTTTACTATATTT\t1\n+TCTTTTTTTTAATACTTATTTTCATT\t1\n+TAAGTTTTTAATCATTTTTTTT\t1\n+TGAGAATGACTTCTTCACGATCTCTT\t1\n+AATTTATTTAATTTATATTCTAACTAA\t1\n+AAAAAATATCTTTTTTAACTCGTGGCC\t1\n+AAGACAACAATGACATATAAGACG\t1\n+TGAGCTAGAACTGCACCCACTCCA\t1\n+ACTAAACTTTTCTT'..b'TCATTTTAC\t1\n-TATTATCATCTCGTTCTTCCTTCTC\t1\n+TACAGACAACACATACGGACTTAA\t1\n+GAAGAGGAGGAGGAGTTTGTAAG\t1\n+TTACAATCTACTATTCTTTTATTA\t1\n+TTATTACATCGTCCACATATAACAAAA\t1\n+TTTTTAACTCATTTTACAATTAAAC\t1\n+AAAACCCGGACAAACCATCGGAGGA\t1\n+CAACACATGACGCGACAATTCTTG\t1\n+TACACACTCATCAACCAAAGTACGTA\t1\n TTTTCATTTCTTCTTCAAATCCTTT\t1\n-TAGTCATACATACCTAATTATACATA\t1\n-ATTTTACTTCATCATTTTC\t1\n-TCTCTTTTATTTTTATCTTTCCTT\t1\n-GCCGGGGCGTGAGATGTCTGCATTA\t1\n-AGGATTTTTAAGCCCATATGTTTCC\t1\n-CAAGATATGAACAAAGCAAAGACAC\t1\n-CAACACATGACGCGACAATTCTTG\t1\n-CAAATAACAAACTGAATAAACGAAA\t1\n-TGAGAATGACTTCTTCACGATCTCTT\t1\n-TCTTATTATCATTTTTTTATCCCTT\t1\n-TCAAATGCAAATTGGATTTATGA\t1\n-CCTTACTCAACATACTTAATCATACTTA\t1\n-TAGACTTTCTACTCATTATTAC\t1\n-TGAAACTGAAACTAACATACAAAATATT\t1\n-AAAACCCGGACAAACCATCGGAGGA\t1\n-TACAGACAACACATACGGACTTAAGT\t1\n-TATTTCAGCAACAGACTAAGACTAA\t1\n-AACTTTAAATTTTTAATAACCTT\t1\n-TATTTATAAATTTTTTCTTGAGAC\t1\n-TTAATATGTAATTTCATACCTCAC\t1\n-CACAGACTGAGGCAGAAAAAACAA\t1\n-TAAAGAAGAAGAATTGATTTTAAT\t1\n-TACTGAAAACGGGCGCATATCAGTGG\t1\n-TCAGTCTTTTTTTCTCTCCTA\t1\n-TATAATTTTATTTTATATTTTCTCT\t1\n-NATTCTTACTCCATTTCAATTTACT\t1\n-TTGTAAAACATTCTTTCTCCTGAC\t1\n-TAATTACCATTGCTAACTATCCA\t1\n-TTCTTCCTTTTATCCTCTCTTAA\t1\n-TCTAAACACCCACGAAAATCTCTTAC\t1\n-AAAAACACACAGACACAAGCAGCAAT\t1\n-CGGACGGTATATTTTTTAATATAA\t1\n-TATGGAGAAACAGCGATATAAGTCA\t1\n-TACAACTAACATCCTTTCTTCTTCC\t1\n-AACTCTCTAATTTAACTTTGTGC\t1\n-TCCTGAGGACGAGGGGCGTTTAGC\t1\n-TATTTCCAACCTTCAACCTCAAATAA\t1\n-TGGACGGAGAACTGATAAGGGC\t1\n-TTTAAGACTTATGAGCTTG\t1\n-TTAAAGACGCAACAACTAACATT\t1\n+AACAACTGCAAACATCTACCACA\t1\n+TAGTTTTAAATATTTCTTTTTTTC\t1\n+AAAGACAAAAGAAATACAGGCACT\t1\n+TTTGATACCTTTATACCATACCTATT\t1\n+TTCTAGCACAACACGCACACATATA\t1\n+TAATCAAAAAACTCTTCATTTTTA\t1\n TAGGAACTTCATACCGGTCTC\t1\n-CGATATTTTCTCCTCTTACC\t1\n-GAGGATTAAAAGAACGGTTTATAA\t1\n-GAATGATCGCACCACCACCTCAACGTT\t1\n-TTTTCTTTACCCATCTTTACTTTCCC\t1\n-AAGACAACAATGACATATAAGACG\t1\n-TAATAATTTAAATAAATATAAATTT\t1\n-TACTGAAACAAGGAAACACAAGC\t1\n-TCAGAAGAACAGAGAATTGATTTT\t1\n-CATACCTTAAATTATCTCTTTCTT\t1\n-TTCTTTTACTACATATTTTTTATTTTT\t1\n-AAAAAATATCTTTTTTAACTCGTGGCC\t1\n-TAACAAATAGAACGTTCTAATTTAAA\t1\n-TAGTTACCTTCATATCTCTCTTTA\t1\n-TAAAATTGTAATATTTAAATAATAT\t1\n-AAAAGGAAAAACAGAAAAATTGGG\t1\n-AGATGTTGATCTAAACTCTCCCA\t1\n-TACCTCTTTATTAACCTCCACCTCTA\t1\n-TTTCCGACAAATACACCATCTTC\t1\n-ACAAATCATAAATTTTTTTTTACT\t1\n-GACGAAACGCAACAACAAAATGGACG\t1\n-TACAAATTTTTTTTTCTTTCTTAT\t1\n-TACACCTCTTTTTACTTTTTTATT\t1\n-TATGGATTATTTCAAAATTTTTTTTT\t1\n-TTCTAGCACAACACGCACACATATA\t1\n-TAACTACTTTTACATTAATACTAA\t1\n-TCTCATCTTACAATTTTTTAAAACTT\t1\n-TTCTTGGACTACACATTTTTTATTGTTTTA\t1\n-TACACACTCATCAACCAAAGTACGTA\t1\n-TACTATATACTTCTTCAAATCACA\t1\n-TCAGAGTTCTACAGGTCCTACGATT\t1\n-TGATTTACTTACATTCTTTTTTT\t1\n-CCATATATGACTGACTCATTTCAC\t1\n-GAAGAGGAGGAGGAGTTTGTAAG\t1\n-AAAGACAAAAGAAATACAGGCACT\t1\n-TACAAGACTAAAACAAACGTGAAGT\t1\n-TAACGGAGCACGAGAACGAAGTGG\t1\n-CTTCTTTTACTACATATTTTTTATTTTTTTA\t1\n-TAATAAGAAACTGTTCAAACAATCCAC\t1\n-TGAGCGGAGAACCAGAGTTGATGAGC\t1\n-TATTATTTTTTTATTCCATTCATAT\t1\n-TTTATTACTTAGTCATAATTCCAA\t1\n-TTTTATATTTCCTTATATCTTTACTA\t1\n-AACGGGGAATAAGGGTTCG\t1\n-AATCTACAATTTCCATTACGACTCC\t1\n-CCGACCGAGCAAATAAACACAGGAACG\t1\n-TCCACAACAACTCTATCTAAAGCATT\t1\n-TTCTTGATAACGCATCTTCTACAT\t1\n-TGCTTGGACTACATATGGTTGAGGG\t1\n-CAGATTCACTGATTTTCTTACGCC\t1\n-TTTGTTTTTCATTTTTTTATCTTT\t1\n-CTATATTTTCTCTCTTACC\t1\n-TAACCTTGCAGAACTATACGATTCAAA\t1\n-TAAGAAACTGAGCTAACGCAATGTACC\t1\n-TTCTTTTACTACATATTTTTTATTTTTTTA\t1\n-TATCTATCTTTGATCTTCTTTTCA\t1\n-TAATAAATTATTAAATAAAAAAAAAA\t1\n-TTTTTTATCAATTTTCACCATTCAT\t1\n-TATTTCACTTTATACTTCCTTAA\t1\n-TAGTTTTAAATATTTCTTTTTTTC\t1\n-TTCTTTTACTACATATTGTTTATTTTTTTA\t1\n-GAGAATAAATATTTCAATGGTCTATTG\t1\n-CGATATTTTCTCCTCTTACCT\t1\n-CACGACTTTATTCTTTTTATCTCA\t1\n-TAGTGGACTTTAAAAAAAAAAAAAAAAAA\t1\n-CATAATATAAACTTATCTT\t1\n-ATGAAATTCGAACAATACGTC\t1\n-AACAACTGCAAACATCTACCACA\t1\n-TAAAAATAATTGTCTTTAATTTCA\t1\n-CGCAACCAGCAGCAACTCCTAGCAT\t1\n-ATTATTAATAAATTATTATAA\t1\n-CATTAATTCATCCATTTAAACTAA\t1\n-TCTTATTTTAATCTTCCAATTTC\t1\n-CTAGACAAGATGCTATAAATTTTAAA\t1\n-TGACCAAAGACAAACAAACAATAAATA\t1\n-TTTTTATCAATTTTCACCATTC\t1\n-TAAGTTTTTAATCATTTTTTTT\t1\n-TAATCAAAAAACTCTTCATTTTTA\t1\n-TACAAACGGAACTTTCGTCATAA\t1\n-TTTTCTTTTTTTCATTTTCTCTTTTA\t1\n-TAGCCTTTACTAGGCTTTTTCTAA\t1\n-TTAGTATTAATCTTCACTTAA\t1\n-TAAAATAAACCAAAACCCAAAAAT\t1\n+TATTTCAGCAACAGACTAAGACTAA\t1\n'