| Previous changeset 2:9457a20156db (2015-10-12) Next changeset 4:516b97a23d7e (2023-08-10) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_formatter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1 |
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modified:
fasta_formatter.xml |
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added:
macros.xml |
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removed:
tool_dependencies.xml |
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| diff -r 9457a20156db -r 859422bcb689 fasta_formatter.xml --- a/fasta_formatter.xml Mon Oct 12 10:15:31 2015 -0400 +++ b/fasta_formatter.xml Tue May 08 13:25:51 2018 -0400 |
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| @@ -1,8 +1,9 @@ -<tool id="cshl_fasta_formatter" version="1.0.0" name="FASTA Width"> +<tool id="cshl_fasta_formatter" version="1.0.1" name="FASTA Width"> <description>formatter</description> - <requirements> - <requirement type="package" version="0.0.13">fastx_toolkit</requirement> - </requirements> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> <!-- Note: fasta_formatter also has a tabular output mode (-t), @@ -12,18 +13,18 @@ So this XML tool only changes the width (line-wrapping) of a FASTA file. --> - <command> -<![CDATA[ -zcat -f < '$input' | fasta_formatter -w $width -o '$output' -]]> - </command> + <command detect_errors="exit_code"><![CDATA[ +@CATS@ fasta_formatter +-w $width +-o '$output' + ]]></command> <inputs> - <param format="fasta" name="input" type="data" label="Library to re-format" /> + <expand macro="fasta_input" /> <param name="width" type="integer" value="0" label="New width for nucleotides strings" help="Use 0 for single line out." /> </inputs> <outputs> - <data format="fasta" name="output" metadata_source="input" /> + <data name="output" format="fasta" metadata_source="input" /> </outputs> <tests> <test> @@ -39,7 +40,7 @@ <output name="output" file="fasta_formatter2.out" /> </test> </tests> - <help> + <help><![CDATA[ **What it does** This tool re-formats a FASTA file, changing the width of the nucleotides lines. @@ -85,5 +86,6 @@ This tool is based on `FASTX-toolkit`__ by Assaf Gordon. .. __: http://hannonlab.cshl.edu/fastx_toolkit/ - </help> + ]]></help> + <expand macro="citations" /> </tool> |
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| diff -r 9457a20156db -r 859422bcb689 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue May 08 13:25:51 2018 -0400 |
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| @@ -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> |
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| diff -r 9457a20156db -r 859422bcb689 tool_dependencies.xml --- a/tool_dependencies.xml Mon Oct 12 10:15:31 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -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> |