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GAG_wrapper.xml
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GAG_wrapper.xml
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<tool id="GAG_wrapper" name="GFF to TBL Converter" version="0.0.1">
<description>
<![CDATA[
Convert a GFF and corresponding fasta file into NCBI's .tbl format.
]]>
</description>
<macros>
<import>gff_sqlite_tool_macros.xml</import>
</macros>
<expand macro="requirements" />
<expand macro="stdio" />
<command interpreter="python">
<![CDATA[
GAG/gag.py
#if $gff_in and $gff_in is not None:
--gff "$gff_in"
#end if
#if $fasta_in and $fasta_in is not None:
--fasta "$fasta_in"
#end if
#if $task_selector.selections == "show_advanced":
#if $task_selector.anno_in and $task_selector.anno_in is not None:
--anno "$task_selector.anno_in"
#end if
--out "gag_output"
$task_selector.fixStartStop
$task_selector.fixTerminalNs
#if $task_selector.rcs and $task_selector.rcs is not None:
-rcs "$task_selector.rcs"
#end if
#if $task_selector.rcl and $task_selector.rcl is not None:
-rcl "$task_selector.rcl"
#end if
#if $task_selector.res and $task_selector.res is not None:
-res "$task_selector.res"
#end if
#if $task_selector.rel and $task_selector.rel is not None:
-rel "$task_selector.rel"
#end if
#if $task_selector.ris and $task_selector.ris is not None:
-ris "$task_selector.ris"
#end if
#if $task_selector.ril and $task_selector.ril is not None:
-ril "$task_selector.ril"
#end if
#if $task_selector.rgs and $task_selector.rgs is not None:
-rgs "$task_selector.rgs"
#end if
#if $task_selector.rgl and $task_selector.rgl is not None:
-rgl "$task_selector.rgl"
#end if
#if $task_selector.fcs and $task_selector.fcs is not None:
-fcs "$task_selector.fcs"
#end if
#if $task_selector.fcl and $task_selector.fcl is not None:
-fcl "$task_selector.fcl"
#end if
#if $task_selector.fes and $task_selector.fes is not None:
-fes "$task_selector.fes"
#end if
#if $task_selector.fel and $task_selector.fel is not None:
-fel "$task_selector.fel"
#end if
#if $task_selector.fis and $task_selector.fis is not None:
-fis "$task_selector.fis"
#end if
#if $task_selector.fil and $task_selector.fil is not None:
-fil "$task_selector.fil"
#end if
#if $task_selector.fgs and $task_selector.fgs is not None:
-fgs "$task_selector.fgs"
#end if
#if $task_selector.fgl and $task_selector.fgl is not None:
-fgl "$task_selector.fgl"
#end if
#end if
]]>
</command>
<inputs>
<param name="gff_in" type="data" format="gff" label="Input GFF file" help="(--gff)" />
<param name="fasta_in" type="data" format="fasta" label="Input fasta file" help="(--fasta) Should be associated with the GFF file." />
<conditional name="task_selector">
<param name="selections" type="select" label="Advanced Options." >
<option value="hide_advanced" selected="True" > Hide Advanced Options </option>
<option value="show_advanced" > Show Advanced Options </option>
</param>
<when value="show_advanced">
<param name="anno_in" type="data" format="tabular" optional="True" label="Input annotation file" help="(--anno) Annotation file for adding functional annotations." />
<param name="fixStartStop" type="boolean" checked="false" truevalue="--fix_start_stop" falsevalue="" label="Fix CDS start and stop" help="(--fix_start_stop) Adds start and stop codons to CDS without annotated start and stop codons." />
<param name="fixTerminalNs" type="boolean" checked="false" truevalue="--fix_terminal_ns" falsevalue="" label="Remove terminal 'N's" help="(--fix_terminal_ns) Removes 'N's at the beginning or end of a scaffold." />
<param name="rcs" type="integer" value="" optional="True" label="Remove CDS shorter than" help="(-rcs) Removes CDS shorter than the provided value." />
<param name="rcl" type="integer" value="" optional="True" label="Remove CDS longer than" help="(-rcl) Removes CDS longer than the provided value." />
<param name="res" type="integer" value="" optional="True" label="Remove exons shorter than" help="(-res) Removes exons shorter than the provided value." />
<param name="rel" type="integer" value="" optional="True" label="Remove exons longer than" help="(-rel) Removes exons longer than the provided value." />
<param name="ris" type="integer" value="" optional="True" label="Remove introns shorter than" help="(-ris) Removes introns shorter than the provided value." />
<param name="ril" type="integer" value="" optional="True" label="Remove introns longer than" help="(-ril) Removes introns longer than the provided value." />
<param name="rgs" type="integer" value="" optional="True" label="Remove genes shorter than" help="(-rgs) Removes genes shorter than the provided value." />
<param name="rgl" type="integer" value="" optional="True" label="Remove genes longer than" help="(-rgl) Removes genes longer than the provided value." />
<param name="fcs" type="integer" value="" optional="True" label="Flag CDS shorter than" help="(-fcs) Flag CDS shorter than the provided value." />
<param name="fcl" type="integer" value="" optional="True" label="Flag CDS longer than" help="(-fcl) Flag CDS longer than the provided value." />
<param name="fes" type="integer" value="" optional="True" label="Flag exons shorter than" help="(-fes) Flag exons shorter than the provided value." />
<param name="fel" type="integer" value="" optional="True" label="Flag exons longer than" help="(-fel) Flag exons longer than the provided value." />
<param name="fis" type="integer" value="" optional="True" label="Flag introns shorter than" help="(-fis) Flag introns shorter than the provided value." />
<param name="fil" type="integer" value="" optional="True" label="Flag introns longer than" help="(-fil) Flag introns longer than the provided value." />
<param name="fgs" type="integer" value="" optional="True" label="Flag genes shorter than" help="(-fgs) Flag genes shorter than the provided value." />
<param name="fgl" type="integer" value="" optional="True" label="Flag genes longer than" help="(-fgl) Flag genes longer than the provided value." />
</when>
</conditional>
<param name="outputs" type="select" multiple="true" label="Output Selection.">
<option value="tbl_out" selected="True"> NCBI TBL File </option>
<option value="fasta_out" > Input Fasta File </option>
<option value="gff_out" > Valid GFF Input Data </option>
<option value="ignored_out" > Invalid GFF Input Data </option>
<option value="stats_out" > Statistics File </option>
</param>
</inputs>
<outputs>
<data name="tbl_out" format="tabular" from_work_dir="./gag_output/genome.tbl" label="TBL data of ${tool.name} on ${on_string}" >
<filter>'tbl_out' in outputs</filter>
</data>
<data name="fasta_out" format="fasta" from_work_dir="./gag_output/genome.fasta" label="fasta data of ${tool.name} on ${on_string}" >
<filter>'fasta_out' in outputs</filter>
</data>
<data name="gff_out" format="gff" from_work_dir="./gag_output/genome.gff" label="GFF data of ${tool.name} on ${on_string}" >
<filter>'gff_out' in outputs</filter>
</data>
<data name="ignored_out" format="gff" from_work_dir="./gag_output/genome.ignored.gff" label="ignored data of ${tool.name} on ${on_string}" >
<filter>'ignored_out' in outputs</filter>
</data>
<data name="stats_out" format="tabular" from_work_dir="./gag_output/genome.stats" label="stats data of ${tool.name} on ${on_string}" >
<filter>'stats_out' in outputs</filter>
</data>
</outputs>
<tests>
<test>
<param name="gff_in" value="FlyBaseID.gff" />
<param name="fasta_in" value="FlyBase.fna" />
<param name="outputs" value="tbl_out,ignored_out" />
<output name="tbl_out" file="FlyBase.tbl" />
<output name="ignored_out" file="FlyBase.ignored.gff" />
</test>
</tests>
<help>
<![CDATA[
**Overview**
GAG_ can read a genome and write it to the NCBI's .tbl format.
.. _GAG: http://genomeannotation.github.io/GAG/
------
**Input**
The first input file has to be a GFF file.
The second input file has to be a fasta file with sequences associated to the GFF file.
The third input can be a annotation file with functional annotations.
.. class:: warningmark
GAG is very specific with its input data.
Make sure every feature has a unique ID-tag. For this you can use gff_id_editing.
GAG only accepts GFF features, if the 'Seqname' of a feature is the same as name of a feature in the fasta file.
Important is the name between '>' and the first whitespace character in the fasta file.
------
**Output**
The output will be a NCBI .tbl file.
------
**gag parameter list**
The standalone, command-line version of gag uses the following parameters::
--gff [input GFF file name {gff}]
--fasta [input fasta file name {fna/ffn/faa}]
--anno [input annotation file name {annotations}]
--out [output tbl file name {tbl}]
--fix_start_stop fix CDS start and stop
--fix_terminal_ns remove terminal 'N's
-rcs remove cds shorter than
-rcl remove cds longer than
-res remove exons shorter than
-rel remove exons longer than
-ris remove introns shorter than
-ril remove introns longer than
-rgs remove genes shorter than
-rgl remove genes longer than
-fcs flag cds shorter than
-fcl flag cds longer than
-fes flag exons shorter than
-fel flag exons longer than
-fis flag introns shorter than
-fil flag introns longer than
-fgs flag genes shorter than
-fgl flag genes longer than
@CITATION@
]]>
</help>
<expand macro="citations">
<citation type="bibtex">
@ARTICLE{B_Hall_GAG,
Author = {B. Hall, T. DeRego, S. Geib},
keywords = {bioinformatics, cheminformatics, rna, ncbi},
title = {{GAG: the Genome Annotation Generator (Version 1.0)}},
url = {http://genomeannotation.github.io/GAG/}
}
</citation>
</expand>
</tool>