Mercurial > repos > iuc > ucsc_fasplit
diff fasplit.xml @ 0:dc36d50254d8 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/fasplit commit 8b84c1739e31ab884b81e214d72a65f030a5e950
| author | iuc |
|---|---|
| date | Wed, 13 Sep 2017 17:53:57 -0400 |
| parents | |
| children | 71f649c23021 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fasplit.xml Wed Sep 13 17:53:57 2017 -0400 @@ -0,0 +1,114 @@ +<tool id="fasplit" name="faSplit" version="@WRAPPER_VERSION@"> + <description>Split a FASTA file</description> + <macros> + <token name="@WRAPPER_VERSION@">332</token> + </macros> + <requirements> + <requirement type="package" version="@WRAPPER_VERSION@">ucsc-fasplit</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ +mkdir out && +faSplit +$O.split_type +'$input' +#if $O.split_type != 'byname' + $O.count +#end if +out/ + ]]></command> + <inputs> + <param name="input" type="data" format="fasta" label="FASTA file" /> + <conditional name="O"> + <param name="split_type" type="select" label="Split by:"> + <option value="sequence" selected="true">Number of files (for multi sequence FASTA)</option> + <option value="base">Number of files (for single sequence FASTA)</option> + <option value="size">Number of base (for single sequence FASTA)</option> + <option value="byname">By name</option> + </param> + <when value="sequence"> + <param name="count" type="integer" value="10" label="Number of chunks" /> + </when> + <when value="base"> + <param name="count" type="integer" value="10" label="Number of chunks" /> + </when> + <when value="size"> + <param name="count" type="integer" value="100" label="Size of chunks (bp)" /> + </when> + <when value="byname" /> + </conditional> + </inputs> + <outputs> + <collection name="output_list" type="list" label="${tool.name} on ${on_string}"> + <discover_datasets pattern="(?P<designation>.*)\.fa" ext="fasta" directory="out"/> + </collection> + </outputs> + + <tests> + <test> + <param name="input" ftype="fasta" value="CDS.fa" /> + <param name="split_type" value="sequence" /> + <param name="count" value="5" /> + <output_collection name="output_list" type="list"> + <element name="0" file="0.fa" /> + <element name="1" file="1.fa" /> + <element name="2" file="2.fa" /> + <element name="3" file="3.fa" /> + <element name="4" file="4.fa" /> + </output_collection> + </test> + <test> + <param name="input" ftype="fasta" value="CDS.fa"/> + <param name="split_type" value="byname"/> + <output_collection name="output_list" type="list"> + <element name="ENSCAFT00000022939_canisfamiliaris" file="ENSCAFT00000022939_canisfamiliaris.fa" /> + <element name="ENSMUST00000207100_musmusculus" file="ENSMUST00000207100_musmusculus.fa" /> + <element name="ENSSSCT00000014817_susscrofa" file="ENSSSCT00000014817_susscrofa.fa" /> + <element name="ENSCAFT00000022963_canisfamiliaris" file="ENSCAFT00000022963_canisfamiliaris.fa" /> + <element name="ENSMUST00000208839_musmusculus" file="ENSMUST00000208839_musmusculus.fa" /> + <element name="ENSSSCT00000023183_susscrofa" file="ENSSSCT00000023183_susscrofa.fa" /> + <element name="ENSCAFT00000025950_canisfamiliaris" file="ENSCAFT00000025950_canisfamiliaris.fa" /> + <element name="ENSPTRT00000019089_pantroglodytes" file="ENSPTRT00000019089_pantroglodytes.fa" /> + <element name="ENSSSCT00000032764_susscrofa" file="ENSSSCT00000032764_susscrofa.fa" /> + <element name="ENSMUST00000026013_musmusculus" file="ENSMUST00000026013_musmusculus.fa" /> + <element name="ENSPTRT00000034846_pantroglodytes" file="ENSPTRT00000034846_pantroglodytes.fa" /> + <element name="ENSSSCT00000033745_susscrofa" file="ENSSSCT00000033745_susscrofa.fa" /> + <element name="ENSMUST00000040820_musmusculus" file="ENSMUST00000040820_musmusculus.fa" /> + <element name="ENSPTRT00000040520_pantroglodytes" file="ENSPTRT00000040520_pantroglodytes.fa" /> + <element name="ENSSSCT00000035258_susscrofa" file="ENSSSCT00000035258_susscrofa.fa" /> + <element name="ENSMUST00000041588_musmusculus" file="ENSMUST00000041588_musmusculus.fa" /> + <element name="ENSPTRT00000040521_pantroglodytes" file="ENSPTRT00000040521_pantroglodytes.fa" /> + <element name="ENST00000302850_homosapiens" file="ENST00000302850_homosapiens.fa" /> + <element name="ENSMUST00000091291_musmusculus" file="ENSMUST00000091291_musmusculus.fa" /> + <element name="ENSRNOT00000041155_rattusnorvegicus" file="ENSRNOT00000041155_rattusnorvegicus.fa" /> + <element name="ENST00000338702_homosapiens" file="ENST00000338702_homosapiens.fa" /> + <element name="ENSMUST00000100505_musmusculus" file="ENSMUST00000100505_musmusculus.fa" /> + <element name="ENSRNOT00000044009_rattusnorvegicus" file="ENSRNOT00000044009_rattusnorvegicus.fa" /> + <element name="ENST00000340611_homosapiens" file="ENST00000340611_homosapiens.fa" /> + <element name="ENSMUST00000110806_musmusculus" file="ENSMUST00000110806_musmusculus.fa" /> + <element name="ENSRNOT00000064726_rattusnorvegicus" file="ENSRNOT00000064726_rattusnorvegicus.fa" /> + <element name="ENST00000341500_homosapiens" file="ENST00000341500_homosapiens.fa" /> + <element name="ENSMUST00000153440_musmusculus" file="ENSMUST00000153440_musmusculus.fa" /> + <element name="ENSRNOT00000066674_rattusnorvegicus" file="ENSRNOT00000066674_rattusnorvegicus.fa" /> + <element name="ENST00000378069_homosapiens" file="ENST00000378069_homosapiens.fa" /> + <element name="ENSMUST00000163344_musmusculus" file="ENSMUST00000163344_musmusculus.fa" /> + <element name="ENSRNOT00000067448_rattusnorvegicus" file="ENSRNOT00000067448_rattusnorvegicus.fa" /> + <element name="ENST00000421712_homosapiens" file="ENST00000421712_homosapiens.fa" /> + <element name="ENSMUST00000168613_musmusculus" file="ENSMUST00000168613_musmusculus.fa" /> + <element name="ENSSSCT00000008295_susscrofa" file="ENSSSCT00000008295_susscrofa.fa" /> + <element name="ENST00000542639_homosapiens" file="ENST00000542639_homosapiens.fa" /> + <element name="ENSMUST00000173143_musmusculus" file="ENSMUST00000173143_musmusculus.fa" /> + <element name="ENSSSCT00000013404_susscrofa" file="ENSSSCT00000013404_susscrofa.fa" /> + <element name="ENST00000600492_homosapiens" file="ENST00000600492_homosapiens.fa" /> + </output_collection> + </test> + </tests> + <help><![CDATA[ +**What it does** + +`faSplit`_ is a tool to split a single FASTA file into several files. + +.. _faSplit: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/FOOTER.txt + ]]></help> + <citations> + </citations> +</tool>