| Previous changeset 2:bdf1ce174e39 (2015-11-11) Next changeset 4:736b8f6ee456 (2018-08-22) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_clipper commit bbb2e6b6769b03602a8ab97001f88fbec52080a1 |
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modified:
fastx_clipper.xml |
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added:
macros.xml |
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removed:
tool_dependencies.xml |
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| diff -r bdf1ce174e39 -r 85263dc18cec fastx_clipper.xml --- a/fastx_clipper.xml Wed Nov 11 12:38:51 2015 -0500 +++ b/fastx_clipper.xml Tue May 08 13:27:25 2018 -0400 |
| [ |
| @@ -1,23 +1,26 @@ -<tool id="cshl_fastx_clipper" name="Clip" version="1.0.1"> +<tool id="cshl_fastx_clipper" name="Clip" version="1.0.2"> <description>adapter sequences</description> - <requirements> - <requirement type="package" version="0.0.13">fastx_toolkit</requirement> - </requirements> - <command> -<![CDATA[ -zcat -f < '$input' | fastx_clipper -l $minlength -a '$clip_source.clip_sequence' -d $keepdelta -o '$output' -v $KEEP_N $DISCARD_OPTIONS -#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_clipper +-l $minlength +-a '$clip_source.clip_sequence' +-d $keepdelta +-o '$output' +-v +$KEEP_N +$DISCARD_OPTIONS +@FQQUAL@ + ]]></command> <inputs> - <param format="fasta,fastqsanger,fastqsolexa,fastqillumina" name="input" type="data" label="Library to clip" /> + <expand macro="fastx_input" /> - <param name="minlength" type="integer" value="15"> - <label>Minimum sequence length (after clipping, sequences shorter than this length will be discarded)</label> - </param> + <param name="minlength" type="integer" value="15" + label="Minimum sequence length (after clipping, sequences shorter than this length will be discarded" /> <conditional name="clip_source"> <param name="clip_source_list" type="select" label="Source"> @@ -39,10 +42,9 @@ </when> </conditional> - <param name="keepdelta" type="integer" value="0"> - <label>enter non-zero value to keep the adapter sequence and x bases that follow it</label> - <help>use this for hairpin barcoding. keep at 0 unless you know what you're doing.</help> - </param> + <param name="keepdelta" type="integer" value="0" + label="Enter a non-zero value to keep the adapter sequence and x bases that follow it" + help="Use this for hairpin barcoding. keep at 0 unless you know what you're doing" /> <param name="KEEP_N" type="select" label="Discard sequences with unknown (N) bases"> <option value="">Yes</option> @@ -56,7 +58,7 @@ </param> </inputs> <outputs> - <data format_source="input" name="output" metadata_source="input" /> + <data name="output" format_source="input" metadata_source="input" /> </outputs> <tests> <test> @@ -71,7 +73,7 @@ <output name="output" ftype="fastqsolexa" file="fastx_clipper1a.out" /> </test> </tests> - <help> + <help><![CDATA[ **What it does** This tool clips adapters from the 3'-end of the sequences in a FASTA/FASTQ file. @@ -97,5 +99,6 @@ 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 bdf1ce174e39 -r 85263dc18cec macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue May 08 13:27:25 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> |
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| diff -r bdf1ce174e39 -r 85263dc18cec tool_dependencies.xml --- a/tool_dependencies.xml Wed Nov 11 12:38:51 2015 -0500 +++ /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> |