Mercurial > repos > devteam > fastx_renamer
changeset 2:d8a3d31554d7 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
author | iuc |
---|---|
date | Tue, 08 May 2018 13:28:10 -0400 |
parents | 02f8a17a4ebd |
children | 3599f5451ee2 |
files | fastx_renamer.xml macros.xml test-data/fastx_renamer-in1.fastq test-data/fastx_renamer-out1.fastq test-data/input.fastqsolexa test-data/renamed_nt_sequence.fastqsolexa tool_dependencies.xml |
diffstat | 7 files changed, 156 insertions(+), 23 deletions(-) [+] |
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--- a/fastx_renamer.xml Wed Nov 11 12:39:46 2015 -0500 +++ b/fastx_renamer.xml Tue May 08 13:28:10 2018 -0400 @@ -1,19 +1,19 @@ -<tool id="cshl_fastx_renamer" name="Rename sequences" version="0.0.11" > +<tool id="cshl_fastx_renamer" name="Rename sequences" version="@VERSION@+galaxy0" > <description></description> - <requirements> - <requirement type="package" version="0.0.13">fastx_toolkit</requirement> - </requirements> - <command> -<![CDATA[ -zcat -f < '$input' | fastx_renamer -n $TYPE -o '$output' -v -#if $input.ext == "fastqsanger": - -Q 33 -#end if -]]> - </command> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <command detect_errors="exit_code"><![CDATA[ +@CATS@ fastx_renamer +-n $TYPE +-o '$output' +-v +@FQQUAL@ + ]]></command> <inputs> - <param format="fastqsolexa,fasta,fastqsanger" name="input" type="data" label="FASTQ/A Library to rename" /> + <expand macro="fastx_input" /> <param name="TYPE" type="select" label="Rename sequence identifiers to"> <option value="SEQ">Nucleotides sequence</option> @@ -22,11 +22,16 @@ </inputs> <outputs> - <data format_source="input" name="output" metadata_source="input" /> + <data name="output" format_source="input" metadata_source="input" /> </outputs> <tests> + <test> + <param name="input" value="fastx_renamer-in1.fastq" /> + <param name="TYPE" value="SEQ" /> + <output name="output" file="fastx_renamer-out1.fastq" /> + </test> </tests> - <help> + <help><![CDATA[ **What it does** This tool renames the sequence identifiers in a FASTQ/A file. @@ -65,6 +70,6 @@ This tool is based on `FASTX-toolkit`__ by Assaf Gordon. .. __: http://hannonlab.cshl.edu/fastx_toolkit/ - </help> -<!-- FASTQ-to-FASTA is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) --> + ]]></help> + <expand macro="citations" /> </tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue May 08 13:28:10 2018 -0400 @@ -0,0 +1,54 @@ +<?xml version="1.0"?> +<macros> + <token name="@CATS@"> + #if $input.is_of_type('fasta.gz', 'fastqsanger.gz', 'fastqsolexa.gz', 'fastqillumina.gz'): + zcat -f '$input' | + #elif $input.is_of_type('fastqsanger.bz2', 'fastqsolexa.bz2', 'fastqillumina.bz2'): + bzcat -f '$input' | + #else: + cat '$input' | + #end if + </token> + <token name="@FQQUAL@"> + <![CDATA[ + #if $input.is_of_type('fastqsanger', 'fastqsanger.gz', 'fastqsanger.bz2'): + -Q 33 + #elif $input.is_of_type('fastqsolexa', 'fastqsolexa.gz', 'fastqsolexa.bz2', 'fastqillumina', 'fastqillumina.gz', 'fastqillumina.bz2'): + -Q 64 + #end if + ]]> + </token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@VERSION@">fastx_toolkit</requirement> + <yield /> + </requirements> + </xml> + <token name="@VERSION@">0.0.14</token> + <token name="@SANGER@">fastqsanger,fastqsanger.gz,fastqsanger.bz2</token> + <token name="@SOLEXA@">fastqsolexa,fastqsolexa.gz,fastqsolexa.bz2</token> + <token name="@ILLUMINA@">fastqillumina,fastqillumina.gz,fastqillumina.bz2</token> + <token name="@FASTQS@">@SANGER@,@SOLEXA@,@ILLUMINA@</token> + <token name="@FASTAS@">fasta,fasta.gz</token> + <xml name="citations"> + <citations> + <citation type="bibtex"> + @UNPUBLISHED{agordon, + author = "Assaf Gordon", + title = "FASTQ/A short-reads pre-processing tools", + year = "2010", + note = "http://hannonlab.cshl.edu/fastx_toolkit/", + url = "http://hannonlab.cshl.edu/fastx_toolkit/"} + </citation> + </citations> + </xml> + <xml name="fasta_input"> + <param name="input" type="data" format="@FASTAS@" label="Input FASTA file" /> + </xml> + <xml name="fastq_input"> + <param name="input" type="data" format="@FASTQS@" label="Input FASTQ file" /> + </xml> + <xml name="fastx_input"> + <param name="input" type="data" format="@FASTAS@,@FASTQS@" label="Input file in FASTA or FASTQ format" /> + </xml> +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastx_renamer-in1.fastq Tue May 08 13:28:10 2018 -0400 @@ -0,0 +1,36 @@ +@CSHL_3_FC042AGLLWW:1:2:7:203 +GTACGCATGACCGAACCCCCCNCCCCCCAATTGGTT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaaabbXEZabaaaaaaaa]]` +@CSHL_3_FC042AGLLWW:1:2:7:33 +CAATGCCTCCAATTGGTTAATCCCCCTATATATACT ++CSHL_3_FC042AGLLWW:1:2:7:33 +Waaa^aZaaW^U_XaWaa\WMEP^KEZXRPEEEGaa +@CSHL_3_FC042AGLLWW:1:2:7:169 +GCAGCAGGCGCGTCAGAGAGCCCCCCCCCCCCCCCC ++CSHL_3_FC042AGLLWW:1:2:7:169 +a_M^a\Uaaa_M_aaaaaaaaaaaaaaaV\ZUGUUR +@CSHL_3_FC042AGLLWW:1:2:7:1436 +AATTATTTATTAAATTTTAATAATATGGGAGACACT ++CSHL_3_FC042AGLLWW:1:2:7:1436 +a^aaaaaaaaaaaaaaa_U`aaaaa_S_aaaaaVV[ +@CSHL_3_FC042AGLLWW:1:2:7:292 +GGAGAAATACACACAATTGGTTAATCCCCCTATATA ++CSHL_3_FC042AGLLWW:1:2:7:292 +babaaaaaaaUMaaaaaaaaaaa\XEUUEP_]UERE +@CSHL_3_FC042AGLLWW:1:2:7:1819 +AATTCAAACCACCCCAACCCACACACAGAGATACAA ++CSHL_3_FC042AGLLWW:1:2:7:1819 +a\\QVVVLaaLOEXUWUUEKUULEMUEUUKULIQMU +@CSHL_3_FC042AGLLWW:1:2:7:1875 +GCAAAAGAGTAGTGTACCCCCCCCCCCCCCCCCCCC ++CSHL_3_FC042AGLLWW:1:2:7:1875 +aaaaaaaaaXUXXEXaaaaa`_ZaaaaaaaaaXEXU +@CSHL_3_FC042AGLLWW:1:2:8:624 +ACTGCAATTGGTTAATCCCCCTATATAGCGCTGTGG ++CSHL_3_FC042AGLLWW:1:2:8:624 +aa[S^`X`aa_]]OOXMU^_[MU_aaaaaaaaaaaa +@CSHL_3_FC042AGLLWW:1:2:8:250 +TGCCGCGCACACTGATGCAATTGGTTAATCCCCCTA ++CSHL_3_FC042AGLLWW:1:2:8:250 +aaaaaaaa^aaaaaabbb[KXPEU[RXZ^JUKRKXE
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastx_renamer-out1.fastq Tue May 08 13:28:10 2018 -0400 @@ -0,0 +1,36 @@ +@GTACGCATGACCGAACCCCCCNCCCCCCAATTGGTT +GTACGCATGACCGAACCCCCCNCCCCCCAATTGGTT ++GTACGCATGACCGAACCCCCCNCCCCCCAATTGGTT +aab^V^aU]`aa^aZaaabbXEZabaaaaaaaa]]` +@CAATGCCTCCAATTGGTTAATCCCCCTATATATACT +CAATGCCTCCAATTGGTTAATCCCCCTATATATACT ++CAATGCCTCCAATTGGTTAATCCCCCTATATATACT +Waaa^aZaaW^U_XaWaa\WMEP^KEZXRPEEEGaa +@GCAGCAGGCGCGTCAGAGAGCCCCCCCCCCCCCCCC +GCAGCAGGCGCGTCAGAGAGCCCCCCCCCCCCCCCC ++GCAGCAGGCGCGTCAGAGAGCCCCCCCCCCCCCCCC +a_M^a\Uaaa_M_aaaaaaaaaaaaaaaV\ZUGUUR +@AATTATTTATTAAATTTTAATAATATGGGAGACACT +AATTATTTATTAAATTTTAATAATATGGGAGACACT ++AATTATTTATTAAATTTTAATAATATGGGAGACACT +a^aaaaaaaaaaaaaaa_U`aaaaa_S_aaaaaVV[ +@GGAGAAATACACACAATTGGTTAATCCCCCTATATA +GGAGAAATACACACAATTGGTTAATCCCCCTATATA ++GGAGAAATACACACAATTGGTTAATCCCCCTATATA +babaaaaaaaUMaaaaaaaaaaa\XEUUEP_]UERE +@AATTCAAACCACCCCAACCCACACACAGAGATACAA +AATTCAAACCACCCCAACCCACACACAGAGATACAA ++AATTCAAACCACCCCAACCCACACACAGAGATACAA +a\\QVVVLaaLOEXUWUUEKUULEMUEUUKULIQMU +@GCAAAAGAGTAGTGTACCCCCCCCCCCCCCCCCCCC +GCAAAAGAGTAGTGTACCCCCCCCCCCCCCCCCCCC ++GCAAAAGAGTAGTGTACCCCCCCCCCCCCCCCCCCC +aaaaaaaaaXUXXEXaaaaa`_ZaaaaaaaaaXEXU +@ACTGCAATTGGTTAATCCCCCTATATAGCGCTGTGG +ACTGCAATTGGTTAATCCCCCTATATAGCGCTGTGG ++ACTGCAATTGGTTAATCCCCCTATATAGCGCTGTGG +aa[S^`X`aa_]]OOXMU^_[MU_aaaaaaaaaaaa +@TGCCGCGCACACTGATGCAATTGGTTAATCCCCCTA +TGCCGCGCACACTGATGCAATTGGTTAATCCCCCTA ++TGCCGCGCACACTGATGCAATTGGTTAATCCCCCTA +aaaaaaaa^aaaaaabbb[KXPEU[RXZ^JUKRKXE
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input.fastqsolexa Tue May 08 13:28:10 2018 -0400 @@ -0,0 +1,4 @@ +@CSHL_4_FC042GAMMII_2_1_517_596 +GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT ++CSHL_4_FC042GAMMII_2_1_517_596 +40 40 40 40 40 40 40 40 40 40 38 40 40 40 40 40 14 40 40 40 40 40 36 40 13 14 24 24 9 24 9 40 10 10 15 40 \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/renamed_nt_sequence.fastqsolexa Tue May 08 13:28:10 2018 -0400 @@ -0,0 +1,4 @@ +@GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT +GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT ++GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT +40 40 40 40 40 40 40 40 40 40 38 40 40 40 40 40 14 40 40 40 40 40 36 40 13 14 24 24 9 24 9 40 10 10 15 40
--- a/tool_dependencies.xml Wed Nov 11 12:39:46 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="fastx_toolkit" version="0.0.13"> - <repository changeset_revision="ec66ae4c269b" name="package_fastx_toolkit_0_0_13" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency>