comparison dia_umpire_quant.xml @ 3:6caa9011f245 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f

2:b4f82d15cac0

<tool id="dia_umpire_quant" name="DIA_Umpire_Quant" version="@VERSION@.0">
    <description>DIA quantitation and targeted re-extraction</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <command>
<![CDATA[

#for $input in $pepxml_inputs:
&& ln -s $input ${work_path}/${input.name}
#end for
## Make sure pep.xml and prot.xml start with "interact-"
## && echo "# $quant_params" >> $dia_umpire_quant 
&& dia_umpire_quant $quant_params 
&& cp $work_path/ProtSummary*.xls "$ProtSummary"
&& cp $work_path/PeptideSummary*.xls "$PeptideSummary"
&& cp $work_path/FragSummary*.xls "$FragSummary"
&& cp $work_path/IDNoSummary*.xls "$IDNoSummary"
&& cat $work_path/*.log "$logfile"

3:6caa9011f245

<tool id="dia_umpire_quant" name="DIA_Umpire_Quant" version="@VERSION@.0">
    <description>DIA quantitation and targeted re-extraction</description>
    <macros>
        <import>dia_umpire_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <command>
<![CDATA[

#for $input in $pepxml_inputs:
&& ln -s $input ${work_path}/${input.name}
#end for
## Make sure pep.xml and prot.xml start with "interact-"
## && echo "# $quant_params" >> $dia_umpire_quant 
&& java -jar \$DIA_UMPIRE_QUANT_JAR $quant_params 
&& cp $work_path/ProtSummary*.xls "$ProtSummary"
&& cp $work_path/PeptideSummary*.xls "$PeptideSummary"
&& cp $work_path/FragSummary*.xls "$FragSummary"
&& cp $work_path/IDNoSummary*.xls "$IDNoSummary"
&& cat $work_path/*.log "$logfile"