Mercurial > repos > peterjc > fastq_paired_unpaired
diff tools/fastq_paired_unpaired/fastq_paired_unpaired.xml @ 8:8cbc866b72ce draft
"Update all the pico_galaxy tools on main Tool Shed"
author | peterjc |
---|---|
date | Fri, 16 Apr 2021 22:36:15 +0000 |
parents | 2709a0f065c9 |
children | 422724644e24 |
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--- a/tools/fastq_paired_unpaired/fastq_paired_unpaired.xml Tue May 16 08:53:57 2017 -0400 +++ b/tools/fastq_paired_unpaired/fastq_paired_unpaired.xml Fri Apr 16 22:36:15 2021 +0000 @@ -1,5 +1,5 @@ <tool id="fastq_paired_unpaired" name="Divide FASTQ file into paired and unpaired reads" version="0.1.4"> - <description>using the read name suffices</description> + <description>using the read name suffixes</description> <requirements> <requirement type="package" version="1.0.1">galaxy_sequence_utils</requirement> <requirement type="package" version="1.67">biopython</requirement> @@ -17,7 +17,7 @@ $output_singles </command> <inputs> - <param name="input_fastq" type="data" format="fastq" label="FASTQ file to divide into paired and unpaired reads"/> + <param name="input_fastq" type="data" format="foobar" label="FASTQ file to divide into paired and unpaired reads"/> <conditional name="output_choice_cond"> <param name="output_choice" type="select" label="How to output paired reads?"> <option value="separate">Separate (two FASTQ files, for the forward and reverse reads, in matching order).</option> @@ -65,7 +65,7 @@ The input file should be a valid FASTQ file which has been sorted so that any partner forward+reverse reads are consecutive. The output files all preserve this sort order. Pairing are recognised based on standard name -suffices. See below or run the tool with no arguments for more details. +suffixes. See below or run the tool with no arguments for more details. Any reads where the forward/reverse naming suffix used is not recognised are treated as orphan reads. The tool supports the /1 and /2 convention @@ -75,7 +75,7 @@ with the fragment number in the description, for example: * @HWI-ST916:79:D04M5ACXX:1:1101:10000:100326 1:N:0:TGNCCA - * @HWI-ST916:79:D04M5ACXX:1:1101:10000:100326 2:N:0:TGNCCA + * @HWI-ST916:79:D04M5ACXX:1:1101:10000:100326 2:N:0:TGNCCA Note that this does support multiple forward and reverse reads per template (which is quite common with Sanger sequencing), e.g. this which is sorted @@ -106,7 +106,7 @@ Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013). Galaxy tools and workflows for sequence analysis with applications in molecular plant pathology. PeerJ 1:e167 -http://dx.doi.org/10.7717/peerj.167 +https://doi.org/10.7717/peerj.167 This tool is available to install into other Galaxy Instances via the Galaxy Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/fastq_paired_unpaired