Mercurial > repos > bebatut > fasta_add_barcode

changeset 2:2ca5fde7a2bb draft default tip

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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/fasta_add_barcode commit e857f7126443e115f11954085423f8999bc870aa-dirty
author bebatut
date Fri, 15 Apr 2016 06:01:42 -0400
parents 0ea7700e08ba
children
files fasta_add_barcode.xml test-data/input_sequences.fasta test-data/mapping_file.txt test-data/output_test.fasta
diffstat 4 files changed, 83 insertions(+), 6 deletions(-) [+]
line wrap: on
line diff
--- a/fasta_add_barcode.xml	Tue Apr 12 03:00:11 2016 -0400
+++ b/fasta_add_barcode.xml	Fri Apr 15 06:01:42 2016 -0400
@@ -3,7 +3,6 @@
     <description>to FASTA sequences</description>
 
     <requirements>
-        <requirement type='package' version="1.0">fasta_add_barcode</requirement>
     </requirements>
 
     <stdio>
@@ -38,9 +37,9 @@
 
     <tests>
         <test>
-            <param name="sequence_file" value="input_sequence_file"/>
-            <param name="mapping_file" value="mapping_file"/>
-            <param name="output_sequence_file" value="output_sequence_file" />
+            <param name="sequence_file" value="input_sequences.fasta"/>
+            <param name="mapping_file" value="mapping_file.txt"/>
+            <output name="output_sequence_file" file="output_test.fasta" />
         </test>
     </tests>
 
@@ -49,8 +48,8 @@
 **What it does**
 
 This tool takes a FASTA file and add at the beginning of each sequence a barcode.
-The barcode of each sequence is determined given sequence identifier and the mapping 
-file.
+
+The barcode of each sequence is determined given its sequence identifier. The mapping between sequence identifier and corresponding barcode is defined inside the mapping file. This file must be a tabular delimited file with two columns: the first with sequence identifiers and the second the corresponding barcode.
 
 ]]>
     </help>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input_sequences.fasta	Fri Apr 15 06:01:42 2016 -0400
@@ -0,0 +1,38 @@
+>SRR029699.4565 EXRA6YY02A66ZM
+ACGGCTCGGTGCCGTCCACCGGTCAGCGGCGCCCTGGCCTCCCACGGGCTGACCCCGCAG
+TACTCTCGGCGCGATGGGGCTTAGCTTCCGGGTTCGGAACGGGACCGGGCGTGCCCC
+>SRR029699.5673 EXRA6YY02A5CA6
+GACCAGAACAACGCCGAAGATCAAAACGGTGAAAACAACGGCGAACAGGGAGGAAACGAA
+TAATGAAGAAGCTTGTTCTTTTAGCCCTCGGGGCCTTATTGTTAGCGGGCGCCACCTGCT
+CTCCCACACCGTCTCCAGTGCAGTACCATCGGCCGCTTGGGTCTTAACCATCGTGTTCGG
+GATGGGAACGGGTGTGTCCCCCAAGCGCATCGCCACCAGCAGTAGTTATCCTAGTTTTTG
+AAACTGTTAAAGTCTACGGCTCATCGTCCGTTACCTTAATAACTAAACAGTACGTAAAAC
+CC
+>SRR029699.5714 EXRA6YY02A735O
+ATCCCGAACACGATGGTAAAGACCTAAGCGGCCGATGGTACTGCACTGGAGACGGTGTGG
+GAGAGTAGGTGGCCGCCAAATTAAAAAGAAAATAAACCGAGAGGTTCTGCGATAAAGCTG
+GTCTTCACCAGTGATCAGAGTTTAAAAGAAAGCTTTTAGTCTCTGATGACTGATGAAAAA
+GTCAGTCAGATGAAGAACTGAATAAGGACTTCATCTTATGTACCTTGAAAACTGCATATA
+GTAAAAATCAATAGATTTAGATAAATA
+>SRR029699.14351 EXRA6YY04CD0L5
+CGGTGGCGATGCGCTTTTGGGAAACACCCGTCCACATCCCGAACACGATGGTTAAGACTG
+AAGCGGCCGATAATACTATACTGGTAACGGTATGGGAAGGTAGGTGGCTGCCGGATTTAT
+AAAGAACAGCATAGCATATATGCTTTCAAAATAGAACAGGCTCGAAAGAGCTAACCTACA
+TCAGCAGGGAAGTGCTGTTTAGATAGCTGGTTTTACCAGTGATTAGAGTATTTTAAGATA
+TTAAGGTTTCTAATGACTGAATAAAACAG
+>SRR029699.30831 EYTWXA302GEDQR
+GCTTATGGGACACACCCGTTCCCATCCCGAACACGACGGTTAAGACGTAAGCGGCCGATG
+GTACTATGCTGGAGACGGCATGGGAGAGCAGGTGGGTGCCGGACTGAGACACGCAACAGG
+GGATAGGCAAGGCACACAGGGGATAGG
+>SRR029699.33623 EYTWXA302HT3FX
+GACTACGAGGTTGATAGGCACGATGTGTAAGTGGAGCGATCCATTCAGCAAGTGTGTACT
+AATAGATCGAGGGCTTGACCACAATTCGCTTGAATTCTCAAGTCAATGACAAAATGTTAG
+CAGTGATTATTCAGTTTTGAAGGCACGTCCTTCAAGAAATACTGGACAAAGTAAAACAGA
+AATGTTATACTGAACCAGTCATATTGGTCGGTGACGATGACGGTGAGGTTCCACCTGTTC
+CCATTCCGAACACAG
+>SRR029699.38075 EYTWXA302GR8DJ
+ACTTTATCAAGATACCAAGTGGAGAATACGAGATTCGAACTCGTGACCTCCTGCTTGCAA
+GGCAGGCGCTCTCCCAACTGAGCTAATCCCCCAAGGGAATCCGGCAGCCACCTGCTCTCC
+CATGCCATCTCCAGCATAGTACCATCGGCCGCTCAGGTCTTAACCATCGTGTTCGGGATG
+GGAACGGGTGTGTCCCCTGAGCGCATCGCCACCGGAAATATCTTATCAAGTTTTTGCTTG
+ATAACTGAATAAAC
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mapping_file.txt	Fri Apr 15 06:01:42 2016 -0400
@@ -0,0 +1,7 @@
+SRR029699.4565	AAAAAA
+SRR029699.5673	CCCCCC
+SRR029699.5714	TTTTTT
+SRR029699.14351	GGGGGG
+SRR029699.30831	AAAAAA
+SRR029699.33623	CCCCCC
+SRR029699.38075	TTTTTT
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output_test.fasta	Fri Apr 15 06:01:42 2016 -0400
@@ -0,0 +1,33 @@
+>SRR029699.4565
+AAAAAAACGGCTCGGTGCCGTCCACCGGTCAGCGGCGCCCTGGCCTCCCACGGGCTGACC
+CCGCAGTACTCTCGGCGCGATGGGGCTTAGCTTCCGGGTTCGGAACGGGACCGGGCGTGC
+CCC
+>SRR029699.5673
+CCCCCCGACCAGAACAACGCCGAAGATCAAAACGGTGAAAACAACGGCGAACAGGGAGGA
+AACGAATAATGAAGAAGCTTGTTCTTTTAGCCCTCGGGGCCTTATTGTTAGCGGGCGCCA
+CCTGCTCTCCCACACCGTCTCCAGTGCAGTACCATCGGCCGCTTGGGTCTTAACCATCGT
+GTTCGGGATGGGAACGGGTGTGTCCCCCAAGCGCATCGCCACCAGCAGTAGTTATCCTAG
+TTTTTGAAACTGTTAAAGTCTACGGCTCATCGTCCGTTACCTTAATAACTAAACAGTACG
+TAAAACCC
+>SRR029699.5714
+TTTTTTATCCCGAACACGATGGTAAAGACCTAAGCGGCCGATGGTACTGCACTGGAGACG
+GTGTGGGAGAGTAGGTGGCCGCCAAATTAAAAAGAAAATAAACCGAGAGGTTCTGCGATA
+AAGCTGGTCTTCACCAGTGATCAGAGTTTAAAAGAAAGCTTTTAGTCTCTGATGACTGAT
+GAAAAAGTCAGTCAGATGAAGAACTGAATAAGGACTTCATCTTATGTACCTTGAAAACTG
+CATATAGTAAAAATCAATAGATTTAGATAAATA
+>SRR029699.14351
+GGGGGGCGGTGGCGATGCGCTTTTGGGAAACACCCGTCCACATCCCGAACACGATGGTTA
+AGACTGAAGCGGCCGATAATACTATACTGGTAACGGTATGGGAAGGTAGGTGGCTGCCGG
+ATTTATAAAGAACAGCATAGCATATATGCTTTCAAAATAGAACAGGCTCGAAAGAGCTAA
+CCTACATCAGCAGGGAAGTGCTGTTTAGATAGCTGGTTTTACCAGTGATTAGAGTATTTT
+AAGATATTAAGGTTTCTAATGACTGAATAAAACAG
+>SRR029699.30831
+AAAAAAGCTTATGGGACACACCCGTTCCCATCCCGAACACGACGGTTAAGACGTAAGCGG
+CCGATGGTACTATGCTGGAGACGGCATGGGAGAGCAGGTGGGTGCCGGACTGAGACACGC
+AACAGGGGATAGGCAAGGCACACAGGGGATAGG
+>SRR029699.33623
+CCCCCCGACTACGAGGTTGATAGGCACGATGTGTAAGTGGAGCGATCCATTCAGCAAGTG
+TGTACTAATAGATCGAGGGCTTGACCACAATTCGCTTGAATTCTCAAGTCAATGACAAAA
+TGTTAGCAGTGATTATTCAGTTTTGAAGGCACGTCCTTCAAGAAATACTGGACAAAGTAA
+AACAGAAATGTTATACTGAACCAGTCATATTGGTCGGTGACGATGACGGTGAGGTTCCAC
+CTGTTCCCATTCCGAACACAG