Mercurial > repos > galaxyp > openms_qcembedder
diff QCEmbedder.xml @ 0:66aa3156aeb5 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
author | galaxyp |
---|---|
date | Wed, 01 Mar 2017 12:52:50 -0500 |
parents | |
children | 401b56e2b31b |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/QCEmbedder.xml Wed Mar 01 12:52:50 2017 -0500 @@ -0,0 +1,85 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> +<!--Proposed Tool Section: [Utilities]--> +<tool id="QCEmbedder" name="QCEmbedder" version="2.1.0"> + <description>Attaches a table or an image to a given qc parameter.</description> + <macros> + <token name="@EXECUTABLE@">QCEmbedder</token> + <import>macros.xml</import> + </macros> + <expand macro="references"/> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>QCEmbedder + +#if $param_in: + -in $param_in +#end if +#if $param_qp_att_acc: + -qp_att_acc "$param_qp_att_acc" +#end if +#if $param_cv_acc: + -cv_acc "$param_cv_acc" +#end if +#if $param_run: + -run $param_run +#end if +#if $param_name: + -name "$param_name" +#end if +#if $param_plot: + -plot $param_plot +#end if +#if $param_table: + -table $param_table +#end if +#if $param_out: + -out $param_out +#end if +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_force: + -force +#end if +#end if +</command> + <inputs> + <param name="param_in" type="data" format="qcml" optional="True" label="Input qcml file" help="(-in) "/> + <param name="param_qp_att_acc" type="text" size="30" label="Defines the qp cv accession of the qp to which the table/image is attached" help="(-qp_att_acc) "> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + <param name="param_cv_acc" type="text" size="30" label="Defines the cv accession of the attachment" help="(-cv_acc) "> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + <param name="param_run" type="data" format="mzml" optional="True" label="The file that defined the run under which the qp for the attachment is aggregated as mzML file" help="(-run) The file is only used to extract the run name from the file name"/> + <param name="param_name" type="text" size="30" label="If no file for the run was given (or if the target qp is contained in a set), at least a name of the target run/set containing the the qp for the attachment has to be given" help="(-name) "> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + <param name="param_plot" type="data" format="" optional="True" label="If a plot image is to be attached to a qp, this has to be specified here" help="(-plot) "/> + <param name="param_table" type="data" format="tabular" optional="True" label="If a table is to be attached to a qp, this has to be specified here" help="(-table) "/> + <expand macro="advanced_options"> + <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> + </expand> + </inputs> + <outputs> + <data name="param_out" format="qcml"/> + </outputs> + <help>Attaches a table or an image to a given qc parameter. + + +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_QCEmbedder.html</help> +</tool>