genform: genform.xml annotate

annotate genform.xml @ 0:963722c4e1da draft default tip

"planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9"

author	workflow4metabolomics
date	Tue, 08 Oct 2019 05:51:40 -0400
parents
children

rev	line source
0 963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	1 <tool id="genform" name="genform" version="@GENFORM_VERSION@" python_template_version="3.5">
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	2 <description>Generation of molecular formulas by high-resolution MS and MS/MS data</description>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	3 <macros>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	4 <token name="@GENFORM_VERSION@">8</token>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	5 </macros>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	6 <requirements>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	7 <requirement type="package" version="r@GENFORM_VERSION@">genform</requirement>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	8 </requirements>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	9 <command detect_errors="exit_code"><![CDATA[
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	10 genform
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	11 ms='$ms'
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	12 #if $msms
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	13 msms='$msms'
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	14 #end if
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	15 #if $formula_cond.formula_select != 'advanced'
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	16 $formula_cond.formula_select
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	17 #else
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	18 $formula_cond.vsp
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	19 #if str($formula_cond.vsm2mv)
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	20 vsm2mv=$formula_cond.vsm2mv
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	21 #end if
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	22 #if str($formula_cond.vsm2ap2)
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	23 vsm2ap2=$formula_cond.vsm2ap2
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	24 #end if
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	25 #if str($formula_cond.ivsm2mv)
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	26 ivsm2mv=$formula_cond.ivsm2mv
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	27 #end if
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	28 #if str($formula_cond.ivsm2ap2)
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	29 ivsm2ap2=$formula_cond.ivsm2ap2
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	30 #end if
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	31 #end if
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	32 #if str($m)
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	33 m=$m
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	34 #end if
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	35 ion=$ion
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	36 ppm=$ppm
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	37 $msmv
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	38 acc=$acc
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	39 rej=$rej
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	40 thms=$thms
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	41 thmsms=$thmsms
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	42 thcomb=$thcomb
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	43 #if $sort
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	44 $sort
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	45 #end if
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	46 #if $elemfilt_cond.elemfilt_select == 'elem'
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	47 el=#echo "".join(str($elemfilt_cond.el).split(','))
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	48 #elif $elemfilt_cond.elemfilt_select == 'oc'
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	49 oc
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	50 #elif $elemfilt_cond.elemfilt_select == 'fuzzy'
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	51 ff=$elemfilt_cond.ff
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	52 #end if
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	53 $het
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	54 $hcf
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	55 $wm
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	56 $wi_cond.wi
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	57 #if $wi_cond.wi == 'wi=log' and str($wi_cond.exp)
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	58 exp=$wi_cond.exp
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	59 #end if
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	60 $oei
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	61 #if str($dbeexc)
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	62 dbeexc=$dbeexc
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	63 #end if
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	64 #if $output.out_cond.out_select == 'analyze':
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	65 analyze
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	66 $output.out_cond.loss
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	67 $output.out_cond.intens
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	68 #end if
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	69 $output.dbe
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	70 $output.cm
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	71 $output.pc
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	72 $output.sc
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	73 out=out
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	74 #if $addoutput.oms
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	75 oms='$outoms'
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	76 #end if
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	77 #if $addoutput.omsms
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	78 omsms='$outomsms'
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	79 #end if
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	80 #if $addoutput.oclean
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	81 oclean='$outoclean'
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	82 #end if
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	83
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	84 ## for some reason genform prints the file twice if sorting is selected
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	85 ## (once unsorted and once sorted). hence, if soring is enabled just
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	86 ## the lower half of the file is returned
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	87 #if $sort
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	88 &&
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	89 wc=\$(wc -l out \| cut -d" " -f 1 )
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	90 &&
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	91 hwc=\$(echo "\$wc/2" \| bc)
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	92 &&
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	93 tail -n \$hwc > '$out'
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	94 #else
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	95 && cp out '$out'
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	96 #end if
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	97 ]]></command>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	98 <inputs>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	99 <param type="data" argument="ms" label="MS data" format="tabular" help="" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	100 <param type="data" argument="msms" label="MS/MS data (optional)" optional="true" format="tabular" help="" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	101 <conditional name="formula_cond">
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	102 <param type="select" name="formula_select" label="Structural formula existence check" help="Allow only molecular formulas for that at least one structural formula exists or specify advanced restictions, note that the default of genform is 'no existence check'">
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	103 <option value="">No existence check</option>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	104 <option value="exist" selected="true">Only molecular formulas for that at least one structural formula exists (exist)</option>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	105 <option value="exist=mv">Enable multiple valencies for P and S (exist=mv)</option>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	106 <option value="advanced">Advanced</option>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	107 </param>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	108 <when value=""/>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	109 <when value="exist"/>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	110 <when value="exist=mv"/>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	111 <when value="advanced">
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	112 <param type="select" argument="vsp" label="Valency sum parity" help="Even for graphical formulas" >
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	113 <option value="">Use default</option>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	114 <option value="vsp=even">Even</option>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	115 <option value="vsp=odd">Odd</option>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	116 </param>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	117 <param type="integer" argument="vsm2mv" label="Lower bound for valency sum - 2 * maximum valency for graphical formulas" min="0" value="" help="" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	118 <param type="integer" argument="vsm2ap2" label="Lower bound for valency sum - 2 * number of atoms + 2 for graphical connected formulas" min="0" value="" help="" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	119 <param type="integer" argument="ivsm2mv" label="Lower bound for valency sum - 2 * maximum valency for fragment ions" min="0" value="" help="" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	120 <param type="integer" argument="ivsm2ap2" label="Lower bound for valency sum - 2 * number of atoms + 2 for fragment ions" min="0" value="" help="" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	121 </when>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	122 </conditional>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	123 <param type="float" argument="m" label="Experimental molecular mass" min="0" optional="true" help="(default: mass of MS basepeak)" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	124 <param type="select" argument="ion" label="Type of ion measured" help="" >
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	125 <option value="M+H">[M+H]+</option>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	126 <option value="M-H">[M-H]-</option>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	127 <option value="M+e">M+</option>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	128 <option value="M-e">M-</option>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	129 <option value="M+Na">[M+Na]+</option>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	130 </param>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	131 <param type="integer" argument="ppm" label="Accuracy of measurement of MS1" min="0" value="5" help="In parts per million" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	132 <param type="select" argument="msmv" label="MS match value" help="Select output type of the MS match value" >
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	133 <option value="msmv=ndp">Normalized dot product</option>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	134 <option value="msmv=nsse">Normalized sum of squared</option>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	135 <option value="msmv=nsae" selected="true">Absolute errors</option>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	136 </param>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	137 <param type="integer" argument="acc" label="Allowed deviation for full acceptance" min="0" value="2" help="of MS/MS peak in ppm" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	138 <param type="integer" argument="rej" label="Allowed deviation for total rejection" min="0" value="4" help="of MS/MS peak in ppm" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	139 <param type="float" argument="thms" label="Threshold for the MS match value" min="0" max="1" value="0" help="" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	140 <param type="float" argument="thmsms" label="Threshold for the MS/MS match value" min="0" max="1" value="0" help="" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	141 <param type="float" argument="thcomb" label="Threshold for the combined match value" min="0" max="1" value="0" help="" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	142 <param type="select" argument="sort" optional="true" label="Sort generated formulas by" help="" >
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	143 <option value="sort=ppm">Mass deviation in ppm</option>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	144 <option value="sort=msmv">MS match value</option>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	145 <option value="sort=msmsmv">MS/MS match value</option>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	146 <option value="sort=combmv">Combined match value</option>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	147 </param>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	148 <conditional name="elemfilt_cond">
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	149 <param type="select" name="elemfilt_select" label="Chemical element filtering">
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	150 <option value="nofilter">No filter</option>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	151 <option value="elem">By used elements</option>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	152 <option value="oc">Only organic compounds (oc)</option>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	153 <option value="fuzzy">By fuzzy formula</option>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	154 </param>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	155 <when value="nofilter"/>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	156 <when value="elem">
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	157 <param type="select" multiple="true" argument="el" label="Used chemical elements" help="" >
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	158 <option selected="true" value="C">C</option>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	159 <option selected="true" value="N">N</option>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	160 <option selected="true" value="O">O</option>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	161 <option selected="true" value="P">P</option>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	162 <option selected="true" value="S">S</option>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	163 <option selected="true" value="H">H</option>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	164 <option selected="true" value="Cl">Cl</option>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	165 <option selected="true" value="Br">Br</option>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	166 <option selected="true" value="F">F</option>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	167 <option selected="true" value="I">I</option>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	168 <option selected="true" value="Si">Si</option>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	169 </param>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	170 </when>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	171 <when value="oc"/>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	172 <when value="fuzzy">
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	173 <param type="text" argument="ff" checked="false" label="Uses fuzzy formula for limits of element multiplicities" help="" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	174 </when>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	175 </conditional>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	176 <param type="boolean" argument="het" checked="false" truevalue="het" falsevalue="" label="Formulas must have at least one hetero atom" help="" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	177 <param type="boolean" argument="hcf" checked="false" truevalue="hcf" falsevalue="" label="Apply Heuerding-Clerc filter" help="" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	178 <param type="select" argument="wm" label="Weighting of m/z for MS/MS match value" help="" >
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	179 <option value="">No weighting</option>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	180 <option value="wm=lin">Linear</option>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	181 <option value="wm=sqrt">Square root</option>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	182 <option value="wm=log">Logarithmic</option>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	183 </param>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	184 <conditional name="wi_cond">
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	185 <param type="select" argument="wi" label="Intensity weighting for MS/MS match value" help="" >
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	186 <option value="">No weighting</option>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	187 <option value="wi=lin">Linear</option>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	188 <option value="wi=sqrt">Square root</option>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	189 <option value="wi=log">Logarithmic</option>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	190 </param>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	191 <when value=""/>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	192 <when value="wi=lin"/>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	193 <when value="wi=sqrt"/>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	194 <when value="wi=log">
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	195 <param type="float" argument="exp" optional="true" label="Exponent" value="" help="" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	196 </when>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	197 </conditional>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	198 <param type="boolean" argument="oei" checked="false" truevalue="oei" falsevalue="" label="Allow odd electron ions for explaining MS/MS peaks" help="" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	199 <param type="integer" argument="dbeexc" optional="true" label="Excess of double bond equivalent for ions" help="" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	200 <section name="output" title="Output options for main output" expanded="true">
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	201 <conditional name="out_cond">
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	202 <param type="select" name="out_select" label="Write explanations for MS/MS peaks to output" help="" >
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	203 <option value="">no</option>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	204 <option value="analyze">yes</option>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	205 </param>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	206 <when value=""/>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	207 <when value="analyze">
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	208 <param type="boolean" argument="loss" checked="false" truevalue="loss" falsevalue="" label="For analyzing MS/MS peaks write losses instead of fragments" help="" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	209 <param type="boolean" argument="intens" checked="false" truevalue="intens" falsevalue="" label="Write intensities of MS/MS peaks to output" help="" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	210 </when>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	211 </conditional>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	212 <param type="boolean" argument="dbe" checked="false" truevalue="dbe" falsevalue="" label="Write double bond equivalents to output" help="" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	213 <param type="boolean" argument="cm" checked="false" truevalue="cm" falsevalue="" label="Write calculated ion masses to output" help="" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	214 <param type="boolean" argument="pc" checked="false" truevalue="pc" falsevalue="" label="Output match values in percent" help="" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	215 <param type="boolean" argument="sc" checked="false" truevalue="sc" falsevalue="" label="Strip calculated isotope distributions" help="" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	216 </section>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	217 <section name="addoutput" title="Additional output data sets" expanded="true">
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	218 <param type="boolean" argument="oms" checked="false" truevalue="oms" falsevalue="" label="Write scaled MS peaks output" help="" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	219 <param type="boolean" argument="omsms" checked="false" truevalue="omsms" falsevalue="" label="Write scaled MS/MS peaks output" help="" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	220 <param type="boolean" argument="oclean" checked="false" truevalue="oclean" falsevalue="" label="Write MS/MS with only explained peaks" help="" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	221 <param type="boolean" argument="oclean" checked="false" truevalue="oms" falsevalue="" label="Write MS/MS with only explained peaks" help="" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	222 </section>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	223 </inputs>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	224 <outputs>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	225 <data name="out" format="tabular" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	226 <data name="outoms" format="tabular" label="${tool.name} on ${on_string}: MS">
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	227 <filter>addoutput['oms']</filter>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	228 </data>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	229 <data name="outomsms" format="tabular" label="${tool.name} on ${on_string}: MS/MS" >
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	230 <filter>addoutput['omsms']</filter>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	231 </data>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	232 <data name="outoclean" format="tabular" label="${tool.name} on ${on_string}: clean">
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	233 <filter>addoutput['oclean']</filter>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	234 </data>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	235 </outputs>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	236 <tests>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	237 <!-- test with MS input and mostly default values -->
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	238 <test expect_num_outputs="1">
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	239 <param name="ms" ftype="tabular" value="CreatineMs.txt" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	240 <param name="acc" value="20" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	241 <param name="rej" value="40" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	242 <output name="out" ftype="tabular" file="CreatineMs.out"/>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	243 <assert_command>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	244 <has_text text=" ms=" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	245 <not_has_text text=" msms=" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	246 <has_text text=" exist " />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	247 <not_has_text text=" m=" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	248 <has_text text=" ion=M+H " />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	249 <has_text text=" ppm=5 " />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	250 <has_text text=" msmv=nsae " />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	251 <has_text text=" acc=20 " />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	252 <has_text text=" rej=40 " />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	253 <has_text text=" thmsms=0.0 " />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	254 <has_text text=" thmsms=0.0 " />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	255 <has_text text=" thcomb=0.0 " />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	256 <not_has_text text=" sort" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	257 <not_has_text text=" el=" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	258 <not_has_text text=" oc " />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	259 <not_has_text text=" ff=" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	260 <not_has_text text=" het " />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	261 <not_has_text text=" vsp=" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	262 <not_has_text text=" vsp2mv=" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	263 <not_has_text text=" vsm2ap2=" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	264 <not_has_text text=" hcf " />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	265 <not_has_text text=" wm=" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	266 <not_has_text text=" wi=" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	267 <not_has_text text=" exp=" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	268 <not_has_text text=" oei " />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	269 <not_has_text text=" dbeexc=" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	270 <not_has_text text=" ivsm2mv=" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	271 <not_has_text text=" ivsm2ap2=" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	272 <not_has_text text=" oms=" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	273 <not_has_text text=" omsms=" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	274 <not_has_text text=" oclean=" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	275 <not_has_text text=" analyze " />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	276 <not_has_text text=" loss " />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	277 <not_has_text text=" intens " />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	278 <not_has_text text=" dbe " />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	279 <not_has_text text=" cm " />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	280 <not_has_text text=" pc " />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	281 <not_has_text text=" sc " />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	282 </assert_command>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	283 </test>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	284 <!-- test with MS/MS input and non default output options -->
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	285 <test expect_num_outputs="4">
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	286 <param name="ms" ftype="tabular" value="CreatineMs.txt" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	287 <param name="msms" ftype="tabular" value="CreatineMsMs.txt" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	288 <param name="acc" value="20" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	289 <param name="rej" value="40" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	290 <section name="output">
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	291 <conditional name="out_cond">
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	292 <param name="out_select" value="analyze"/>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	293 <param name="loss" value="loss" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	294 <param name="intens" value="intens" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	295 </conditional>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	296 <param name="dbe" value="dbe" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	297 <param name="cm" value="cm" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	298 <param name="pc" value="pc" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	299 <param name="sc" value="sc" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	300 </section>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	301 <section name="addoutput">
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	302 <param name="oms" value="oms" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	303 <param name="omsms" value="omsms" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	304 <param name="oclean" value="oclean" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	305 <param name="oclean" value="oms"/>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	306 </section>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	307 <output name="out" ftype="tabular" file="CreatineMsMs.out"/>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	308 <output name="outoms" ftype="tabular" file="CreatineMsMs-oms.out"/>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	309 <output name="outomsms" ftype="tabular" file="CreatineMsMs-omsms.out"/>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	310 <output name="outoclean" ftype="tabular" file="CreatineMsMs-oclean.out"/>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	311 <assert_command>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	312 <has_text text=" ms=" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	313 <has_text text=" msms=" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	314 <has_text text=" exist" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	315 <not_has_text text=" m=" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	316 <has_text text=" ion=M+H " />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	317 <has_text text=" ppm=5 " />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	318 <has_text text=" msmv=nsae " />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	319 <has_text text=" acc=20 " />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	320 <has_text text=" rej=40 " />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	321 <has_text text=" thmsms=0.0 " />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	322 <has_text text=" thmsms=0.0 " />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	323 <has_text text=" thcomb=0.0 " />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	324 <not_has_text text=" sort" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	325 <not_has_text text=" el=" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	326 <not_has_text text=" oc " />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	327 <not_has_text text=" ff=" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	328 <not_has_text text=" het " />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	329 <not_has_text text=" vsp=" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	330 <not_has_text text=" vsp2mv=" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	331 <not_has_text text=" vsm2ap2=" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	332 <not_has_text text=" hcf " />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	333 <not_has_text text=" wm=" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	334 <not_has_text text=" wi=" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	335 <not_has_text text=" exp=" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	336 <not_has_text text=" oei " />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	337 <not_has_text text=" dbeexc=" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	338 <not_has_text text=" ivsm2mv=" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	339 <not_has_text text=" ivsm2ap2=" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	340 <has_text text=" oms=" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	341 <has_text text=" omsms=" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	342 <has_text text=" oclean=" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	343 <has_text text=" analyze " />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	344 <has_text text=" loss " />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	345 <has_text text=" intens " />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	346 <has_text text=" dbe " />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	347 <has_text text=" cm " />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	348 <has_text text=" pc " />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	349 <has_text text=" sc " />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	350 </assert_command>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	351 </test>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	352 <!-- test with MS/MS input and other non-default values
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	353 (creates empty output .. but test is still usefull) -->
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	354 <test expect_num_outputs="1">
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	355 <param name="ms" ftype="tabular" value="CreatineMs.txt" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	356 <param name="msms" ftype="tabular" value="CreatineMsMs.txt" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	357 <conditional name="formula_cond">
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	358 <param name="formula_select" value=""/>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	359 </conditional>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	360 <param name="m" value="111.0201" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	361 <param name="ion" value="M-H" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	362 <param name="ppm" value="4" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	363 <param name="msmv" value="msmv=ndp"/>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	364 <param name="acc" value="21" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	365 <param name="rej" value="39" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	366 <param name="thms" value="0.3" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	367 <param name="thmsms" value="0.2" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	368 <param name="thcomb" value="0.1" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	369 <param name="sort" value="sort=combmv" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	370 <conditional name="elemfilt_cond">
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	371 <param name="elemfilt_select" value="elem"/>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	372 <param name="el" value="C,N,O,P,S,H,Cl,Br,F,I" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	373 </conditional>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	374 <param name="het" value="het" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	375 <param name="hcf" value="hcf" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	376 <param name="wm" value="wm=sqrt"/>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	377 <conditional name="wi_cond">
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	378 <param name="wi" value="wi=log"/>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	379 <param name="exp" value="2.31"/>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	380 </conditional>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	381 <param name="oei" value="oei" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	382 <param name="dbeexc" value="1" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	383 <output name="out" ftype="tabular" file="CreatineMsMs.out" lines_diff="3"/>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	384 <assert_command>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	385 <has_text text=" ms=" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	386 <has_text text=" msms=" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	387 <not_has_text text=" exist" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	388 <has_text text=" m=111.0201" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	389 <has_text text=" ion=M-H" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	390 <has_text text=" ppm=4" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	391 <has_text text=" msmv=ndp" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	392 <has_text text=" acc=21" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	393 <has_text text=" rej=39" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	394 <has_text text=" thms=0.3" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	395 <has_text text=" thmsms=0.2" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	396 <has_text text=" thcomb=0.1" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	397 <has_text text=" sort=combmv" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	398 <has_text text=" el=CNOPSHClBrFI" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	399 <not_has_text text=" oc " />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	400 <not_has_text text=" ff=" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	401 <has_text text=" het " />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	402 <not_has_text text=" vsp=" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	403 <not_has_text text=" vsp2mv=" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	404 <not_has_text text=" vsm2ap2=" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	405 <has_text text=" hcf " />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	406 <has_text text=" wm=sqrt " />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	407 <has_text text=" wi=log " />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	408 <has_text text=" exp=2.31 " />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	409 <has_text text=" oei " />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	410 <has_text text=" dbeexc=1" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	411 <not_has_text text=" ivsm2mv=" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	412 <not_has_text text=" ivsm2ap2=" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	413 <not_has_text text=" oms=" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	414 <not_has_text text=" omsms=" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	415 <not_has_text text=" oclean=" />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	416 <not_has_text text=" analyze " />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	417 <not_has_text text=" loss " />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	418 <not_has_text text=" intens " />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	419 <not_has_text text=" dbe " />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	420 <not_has_text text=" cm " />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	421 <not_has_text text=" pc " />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	422 <not_has_text text=" sc " />
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	423 </assert_command>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	424 </test>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	425 </tests>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	426 <help><![CDATA[
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	427
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	428 Overview
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	429
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	430 Genform generates candidate molecular formulas from high-resolution
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	431 MS data. It calculates match values (MV) that show how well candidate molecular formulas fit the MS
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	432 isotope peak distributions (MS MV) and the high-resolution MS/MS fragment peak masses (MSMS
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	433 MV). Finally it computes a combined match value from these two scores. This software can be
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	434 regarded as a further development of the ElCoCo and MolForm modules of MOLGEN-MS with a clear
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	435 specialization towards MS/MS.
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	436
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	437 Input
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	438
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	439 MS and MS/MS centroided spectra are given as tab separated files with two columns:
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	440
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	441 1. m/z
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	442 2. intensity
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	443
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	444 Output
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	445
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	446 Main output containing a list of all possible molecular formulas, further options can be chosen:
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	447
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	448 1. if the explained peaks shall also be written to the output
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	449 2. if the explanation shall be given as molecular formulas for the fragment or as neutral losses
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	450 3. double bond equivalents for each molecular formula
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	451 4. calculated ion masses
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	452 5. output match values in percent
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	453
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	454 Output structure:
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	455
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	456 molecular fomula / (double bond equivalent) / (calculated mass) / ppm / MS MV / MSMS MV / combined MV
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	457
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	458 ppm: The value ppm denotes the relative deviation of
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	459 the calculated mass of the molecular ion from the mass of the basepeak (basemass) in the MS in
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	460 parts per million (ppm).
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	461
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	462 MS MV: It is calculated from measured and
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	463 theoretical isotope peak intensities. The MV ranges from 0 to 1. The better theoretical and measured
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	464 isotope distributions fit, the higher is the MV. There are three different algorithms implemented for
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	465 calculating the MS MV, which are nomalized dot product, nomalized sum of squared errors and the normalized sum of absolute errors.
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	466
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	467 MSMS MV: It shows how well the masses of the MS/MS fit possible fragments of the candidate molecular formula. Again, the MS/MS MV is a value
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	468 between 0 and 1, whereby higher values reflect a better fit.
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	469
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	470 combined MV: combined match value
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	471
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	472 Example output:
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	473
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	474 ======== === =========== ====== ======== ========= ========
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	475 C4H9N3O2 2 132.07675 -0.8 96.674 100.000 96.674
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	476 ======== === =========== ====== ======== ========= ========
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	477
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	478 Advanced options
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	479
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	480 For undersanding of the parameters and rules for creating possible molecular formulas, see `the manual of the commandline tool <https://depot.galaxyproject.org/software/molgen_manual/molgen_manual_1.0.1.5_src_all.pdf>`_ for info.
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	481
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	482 ]]></help>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	483
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	484 <citations>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	485 <citation type="doi">10.3390/metabo3020440</citation>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	486 <citation type="bibtex">@article{meringer2011ms,
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	487 title={MS/MS data improves automated determination of molecular formulas by mass spectrometry},
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	488 author={Meringer, Markus and Reinker, Stefan and Zhang, Juan and Muller, Alban},
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	489 journal={MATCH Commun. Math. Comput. Chem},
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	490 volume={65},
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	491 number={2},
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	492 pages={259--290},
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	493 year={2011}
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	494 }</citation>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	495 </citations>
963722c4e1da "planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit d73f3664336def878419e019920d209f3bfb4fa9" workflow4metabolomics parents: diff changeset	496 </tool>

Mercurial > repos > workflow4metabolomics > genform

annotate genform.xml @ 0:963722c4e1da draft default tip