Mercurial > repos > matthias > genform

annotate genform.xml @ 0:f17273aa599f draft default tip

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planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
author matthias
date Thu, 12 Sep 2019 12:20:47 -0400
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f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
parents:
diff changeset
1 <tool id="genform" name="genform" version="@GENFORM_VERSION@" python_template_version="3.5">
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
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2 <description>Generation of molecular formulas by high-resolution MS and MS/MS data</description>
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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3 <macros>
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
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4 <token name="@GENFORM_VERSION@">8</token>
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
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5 </macros>
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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6 <requirements>
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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7 <requirement type="package" version="r@GENFORM_VERSION@">genform</requirement>
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
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8 </requirements>
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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9 <command detect_errors="exit_code"><![CDATA[
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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10 genform
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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11 ms='$ms'
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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12 #if $msms
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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13 msms='$msms'
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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14 #end if
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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15 #if $formula_cond.formula_select != 'advanced'
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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16 $formula_cond.formula_select
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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17 #else
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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18 $formula_cond.vsp
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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19 #if str($formula_cond.vsm2mv) != ''
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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20 vsm2mv=$formula_cond.vsm2mv
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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21 #end if
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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22 #if str($formula_cond.vsm2ap2) != ''
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
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23 vsm2ap2=$formula_cond.vsm2ap2
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
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24 #end if
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
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25 #if str($formula_cond.ivsm2mv) != ''
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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26 ivsm2mv=$formula_cond.ivsm2mv
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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27 #end if
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
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28 #if str($formula_cond.ivsm2ap2) != ''
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
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29 ivsm2ap2=$formula_cond.ivsm2ap2
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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30 #end if
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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31 #end if
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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32 #if str($m) != ''
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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33 m=$m
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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34 #end if
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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35 ion=$ion
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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36 ppm=$ppm
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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37 $msmv
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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38 acc=$acc
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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39 rej=$rej
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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40 thms=$thms
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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41 thmsms=$thmsms
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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42 thcomb=$thcomb
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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43 $sort
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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44 #if $elemfilt_cond.elemfilt_select == 'elem'
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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45 el=#echo "".join(str($elemfilt_cond.el).split(','))
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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46 #elif $elemfilt_cond.elemfilt_select == 'oc'
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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47 oc
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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48 #elif $elemfilt_cond.elemfilt_select == 'fuzzy'
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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49 ff=$elemfilt_cond.fuzzy
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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50 #end if
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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51 $het
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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52 $hcf
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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53 $wm
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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54 $wi_cond.wi
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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55 #if $wi_cond.wi == 'wi=log' and str($wi_cond.exp) != ''
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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56 exp=$wi_cond.exp
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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57 #end if
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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58 $oei
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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59 #if str($dbeexc) != ''
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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60 dbeexc=$dbeexc
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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61 #end if
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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62 #if $output.out_cond.out_select == 'analyze':
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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63 analyze
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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64 $output.out_cond.loss
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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65 $output.out_cond.intens
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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66 #end if
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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67 $output.dbe
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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68 $output.cm
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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69 $output.pc
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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70 $output.sc
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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71 out=out
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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72 #if $addoutput.oms
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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73 oms='$outoms'
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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74 #end if
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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75 #if $addoutput.omsms
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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76 omsms='$outomsms'
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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77 #end if
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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78 #if $addoutput.oclean
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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79 oclean='$outoclean'
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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80 #end if
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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81
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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82 ## for some reason genform prints the file twice if sorting is selected
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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83 ## (once unsorted and once sorted). hence, if soring is enabled just
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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84 ## the lower half of the file is returned
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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85 #if $sort != ''
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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86 &&
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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87 wc=\$(wc -l out | cut -d" " -f 1 )
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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diff changeset
88 &&
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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89 hwc=\$(echo "\$wc/2" | bc)
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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90 &&
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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91 tail -n \$hwc > '$out'
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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92 #else
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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93 && cp out '$out'
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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94 #end if
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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95 ]]></command>
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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96 <inputs>
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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97 <param type="data" argument="ms" label="MS data" format="tabular" help="" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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98 <param type="data" argument="msms" label="MS/MS data" optional="true" format="tabular" help="" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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99 <conditional name="formula_cond">
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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100 <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'">
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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101 <option value="">no existence check</option>
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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102 <option value="exist" selected="true">only molecular formulas for that at least one structural formula exists (exist)</option>
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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103 <option value="exist=mv">enable multiple valencies for P and S (exist=mv)</option>
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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104 <option value="advanced">advanced</option>
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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105 </param>
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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106 <when value=""/>
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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107 <when value="exist"/>
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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108 <when value="exist=mv"/>
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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109 <when value="advanced">
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110 <param type="select" argument="vsp" label="valency sum parity" help="even for graphical formulas" >
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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111 <option value="">use default</option>
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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112 <option value="vsp=even">even</option>
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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113 <option value="vsp=odd">odd</option>
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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114 </param>
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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115 <param type="integer" argument="vsm2mv" label="lower bound for valency sum - 2 * maximum valency for graphical formulas" min="0" value="" help="" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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116 <param type="integer" argument="vsm2ap2" label="lower bound for valency sum - 2 * number of atoms + 2 for graphical connected formulas" min="0" value="" help="" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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117 <param type="integer" argument="ivsm2mv" label="lower bound for valency sum - 2 * maximum valency for fragment ions" min="0" value="" help="" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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118 <param type="integer" argument="ivsm2ap2" label="lower bound for valency sum - 2 * number of atoms + 2 for fragment ions" min="0" value="" help="" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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119 </when>
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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120 </conditional>
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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121 <param type="float" argument="m" label="experimental molecular mass" min="0" optional="true" help="(default: mass of MS basepeak)" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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122 <param type="select" argument="ion" label="type of ion measured" help="" >
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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123 <option value="M+H">[M+H]+</option>
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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124 <option value="M-H">[M-H]-</option>
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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125 <option value="M+e">M+</option>
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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126 <option value="M-e">M-</option>
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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127 <option value="M+Na">[M+Na]+</option>
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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128 </param>
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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129 <param type="integer" argument="ppm" label="accuracy of measurement of MS1" min="0" value="5" help="in parts per million" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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130 <param type="select" argument="msmv" label="MS match value" help="select output type of the MS match value" >
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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131 <option value="msmv=ndp">normalized dot product</option>
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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132 <option value="msmv=nsse">normalized sum of squared</option>
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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133 <option value="msmv=nsae" selected="true">absolute errors</option>
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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134 </param>
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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135 <param type="integer" argument="acc" label="allowed deviation for full acceptance" min="0" value="2" help="of MS/MS peak in ppm" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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136 <param type="integer" argument="rej" label="allowed deviation for total rejection" min="0" value="4" help="of MS/MS peak in ppm" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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137 <param type="float" argument="thms" label="threshold for the MS match value" min="0" max="1" value="0" help="" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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138 <param type="float" argument="thmsms" label="threshold for the MS/MS match value" min="0" max="1" value="0" help="" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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139 <param type="float" argument="thcomb" label="threshold for the combined match value" min="0" max="1" value="0" help="" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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140 <param type="select" argument="sort" label="sort generated formulas by" help="" >
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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141 <option value="">do not sort</option>
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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142 <option value="sort=ppm">mass deviation in ppm</option>
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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143 <option value="sort=msmv">MS match value</option>
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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144 <option value="sort=msmsmv">MS/MS match value</option>
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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145 <option value="sort=combmv">combined match value</option>
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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146 </param>
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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147 <conditional name="elemfilt_cond">
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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148 <param type="select" name="elemfilt_select" label="chemical element filtering">
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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149 <option value="nofilter">no filter</option>
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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150 <option value="elem">by used elements</option>
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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151 <option value="oc">only organic compounds (oc)</option>
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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152 <option value="fuzzy">by fuzzy formula</option>
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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153 </param>
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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154 <when value="nofilter"/>
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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155 <when value="elem">
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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156 <param type="select" multiple="true" argument="el" label="used chemical elements" help="" >
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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157 <option selected="true" value="C">C</option>
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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158 <option selected="true" value="N">N</option>
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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159 <option selected="true" value="O">O</option>
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160 <option selected="true" value="P">P</option>
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161 <option selected="true" value="S">S</option>
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162 <option selected="true" value="H">H</option>
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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163 <option selected="true" value="Cl">Cl</option>
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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164 <option selected="true" value="Br">Br</option>
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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165 <option selected="true" value="F">F</option>
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166 <option selected="true" value="I">I</option>
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167 <option selected="true" value="Si">Si</option>
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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168 </param>
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169 </when>
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170 <when value="oc"/>
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171 <when value="fuzzy">
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172 <param type="text" argument="ff" checked="false" label="uses fuzzy formula for limits of element multiplicities" help="" />
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173 </when>
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174 </conditional>
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175 <param type="boolean" argument="het" checked="false" truevalue="het" falsevalue="" label="formulas must have at least one hetero atom" help="" />
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176 <param type="boolean" argument="hcf" checked="false" truevalue="hcf" falsevalue="" label="apply Heuerding-Clerc filter" help="" />
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177 <param type="select" argument="wm" label="m/z weighting for MS/MS match value" help="" >
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178 <option value="">no weighting</option>
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179 <option value="wm=lin">linear</option>
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180 <option value="wm=sqrt">square root</option>
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181 <option value="wm=log">logarithmic</option>
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182 </param>
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183 <conditional name="wi_cond">
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184 <param type="select" argument="wi" label="intensity weighting for MS/MS match value" help="" >
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185 <option value="">no weighting</option>
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186 <option value="wi=lin">linear</option>
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187 <option value="wi=sqrt">square root</option>
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188 <option value="wi=log">logarithmic</option>
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189 </param>
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190 <when value=""/>
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191 <when value="wi=lin"/>
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192 <when value="wi=sqrt"/>
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193 <when value="wi=log">
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194 <param type="float" argument="exp" optional="true" label="exponent" value="" help="" />
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195 </when>
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196 </conditional>
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197 <param type="boolean" argument="oei" checked="false" truevalue="oei" falsevalue="" label="allow odd electron ions for explaining MS/MS peaks" help="" />
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198 <param type="integer" argument="dbeexc" optional="true" label="excess of double bond equivalent for ions" help="" />
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199 <section name="output" title="output options for main output" expanded="true">
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200 <conditional name="out_cond">
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201 <param type="select" name="out_select" label="write explanations for MS/MS peaks to output" help="" >
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202 <option value="">no</option>
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203 <option value="analyze">yes</option>
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204 </param>
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205 <when value=""/>
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206 <when value="analyze">
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207 <param type="boolean" argument="loss" checked="false" truevalue="loss" falsevalue="" label="for analyzing MS/MS peaks write losses instead of fragments" help="" />
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208 <param type="boolean" argument="intens" checked="false" truevalue="intens" falsevalue="" label="write intensities of MS/MS peaks to output" help="" />
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209 </when>
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210 </conditional>
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211 <param type="boolean" argument="dbe" checked="false" truevalue="dbe" falsevalue="" label="write double bond equivalents to output" help="" />
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212 <param type="boolean" argument="cm" checked="false" truevalue="cm" falsevalue="" label="write calculated ion masses to output" help="" />
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213 <param type="boolean" argument="pc" checked="false" truevalue="pc" falsevalue="" label="output match values in percent" help="" />
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214 <param type="boolean" argument="sc" checked="false" truevalue="sc" falsevalue="" label="strip calculated isotope distributions" help="" />
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215 </section>
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216 <section name="addoutput" title="additional output data sets" expanded="true">
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217 <param type="boolean" argument="oms" checked="false" truevalue="oms" falsevalue="" label="write scaled MS peaks output" help="" />
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218 <param type="boolean" argument="omsms" checked="false" truevalue="omsms" falsevalue="" label="write scaled MS/MS peaks output" help="" />
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219 <param type="boolean" argument="oclean" checked="false" truevalue="oclean" falsevalue="" label="write MS/MS with only explained peaks" help="" />
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220 <param type="boolean" argument="oclean" checked="false" truevalue="oms" falsevalue="" label="write MS/MS with only explained peaks" help="" />
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221 </section>
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222 </inputs>
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223 <outputs>
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224 <data name="out" format="tabular" />
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225 <data name="outoms" format="tabular" label="${tool.name} on ${on_string}: MS">
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226 <filter>addoutput['oms']</filter>
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227 </data>
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228 <data name="outomsms" format="tabular" label="${tool.name} on ${on_string}: MS/MS" >
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229 <filter>addoutput['omsms']</filter>
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230 </data>
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231 <data name="outoclean" format="tabular" label="${tool.name} on ${on_string}: clean">
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232 <filter>addoutput['oclean']</filter>
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233 </data>
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234 </outputs>
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235 <tests>
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236 <!-- test with MS input and mostly default values -->
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237 <test expect_num_outputs="1">
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238 <param name="ms" ftype="tabular" value="CreatineMs.txt" />
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239 <param name="acc" value="20" />
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240 <param name="rej" value="40" />
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241 <output name="out" ftype="tabular" file="CreatineMs.out"/>
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242 <assert_command>
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243 <has_text text=" ms=" />
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244 <not_has_text text=" msms=" />
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245 <has_text text=" exist " />
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246 <not_has_text text=" m=" />
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247 <has_text text=" ion=M+H " />
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248 <has_text text=" ppm=5 " />
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249 <has_text text=" msmv=nsae " />
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250 <has_text text=" acc=20 " />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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251 <has_text text=" rej=40 " />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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252 <has_text text=" thmsms=0.0 " />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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253 <has_text text=" thmsms=0.0 " />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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254 <has_text text=" thcomb=0.0 " />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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255 <not_has_text text=" sort" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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256 <not_has_text text=" el=" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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257 <not_has_text text=" oc " />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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258 <not_has_text text=" ff=" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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259 <not_has_text text=" het " />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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260 <not_has_text text=" vsp=" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
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261 <not_has_text text=" vsp2mv=" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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262 <not_has_text text=" vsm2ap2=" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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263 <not_has_text text=" hcf " />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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264 <not_has_text text=" wm=" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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265 <not_has_text text=" wi=" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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266 <not_has_text text=" exp=" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
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267 <not_has_text text=" oei " />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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268 <not_has_text text=" dbeexc=" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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269 <not_has_text text=" ivsm2mv=" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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270 <not_has_text text=" ivsm2ap2=" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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271 <not_has_text text=" oms=" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
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272 <not_has_text text=" omsms=" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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273 <not_has_text text=" oclean=" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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274 <not_has_text text=" analyze " />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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275 <not_has_text text=" loss " />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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276 <not_has_text text=" intens " />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
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277 <not_has_text text=" dbe " />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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278 <not_has_text text=" cm " />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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279 <not_has_text text=" pc " />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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280 <not_has_text text=" sc " />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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281 </assert_command>
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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282 </test>
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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283 <!-- test with MS/MS input and non default output options -->
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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284 <test expect_num_outputs="4">
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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285 <param name="ms" ftype="tabular" value="CreatineMs.txt" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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286 <param name="msms" ftype="tabular" value="CreatineMsMs.txt" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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287 <param name="acc" value="20" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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288 <param name="rej" value="40" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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289 <section name="output">
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
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290 <conditional name="out_cond">
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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291 <param name="out_select" value="analyze"/>
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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292 <param name="loss" value="loss" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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293 <param name="intens" value="intens" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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294 </conditional>
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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295 <param name="dbe" value="dbe" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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296 <param name="cm" value="cm" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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297 <param name="pc" value="pc" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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298 <param name="sc" value="sc" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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299 </section>
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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300 <section name="addoutput">
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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301 <param name="oms" value="oms" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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302 <param name="omsms" value="omsms" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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303 <param name="oclean" value="oclean" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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304 <param name="oclean" value="oms"/>
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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305 </section>
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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306 <output name="out" ftype="tabular" file="CreatineMsMs.out"/>
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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307 <output name="outoms" ftype="tabular" file="CreatineMsMs-oms.out"/>
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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308 <output name="outomsms" ftype="tabular" file="CreatineMsMs-omsms.out"/>
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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309 <output name="outoclean" ftype="tabular" file="CreatineMsMs-oclean.out"/>
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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310 <assert_command>
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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311 <has_text text=" ms=" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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312 <has_text text=" msms=" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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313 <has_text text=" exist" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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314 <not_has_text text=" m=" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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315 <has_text text=" ion=M+H " />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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316 <has_text text=" ppm=5 " />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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317 <has_text text=" msmv=nsae " />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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318 <has_text text=" acc=20 " />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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319 <has_text text=" rej=40 " />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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320 <has_text text=" thmsms=0.0 " />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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321 <has_text text=" thmsms=0.0 " />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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322 <has_text text=" thcomb=0.0 " />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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323 <not_has_text text=" sort" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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324 <not_has_text text=" el=" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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325 <not_has_text text=" oc " />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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326 <not_has_text text=" ff=" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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327 <not_has_text text=" het " />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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328 <not_has_text text=" vsp=" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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329 <not_has_text text=" vsp2mv=" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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330 <not_has_text text=" vsm2ap2=" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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331 <not_has_text text=" hcf " />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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332 <not_has_text text=" wm=" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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333 <not_has_text text=" wi=" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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334 <not_has_text text=" exp=" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
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335 <not_has_text text=" oei " />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
parents:
diff changeset
336 <not_has_text text=" dbeexc=" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
parents:
diff changeset
337 <not_has_text text=" ivsm2mv=" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
parents:
diff changeset
338 <not_has_text text=" ivsm2ap2=" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
parents:
diff changeset
339 <has_text text=" oms=" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
parents:
diff changeset
340 <has_text text=" omsms=" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
parents:
diff changeset
341 <has_text text=" oclean=" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
parents:
diff changeset
342 <has_text text=" analyze " />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
parents:
diff changeset
343 <has_text text=" loss " />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
parents:
diff changeset
344 <has_text text=" intens " />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
parents:
diff changeset
345 <has_text text=" dbe " />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
parents:
diff changeset
346 <has_text text=" cm " />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
parents:
diff changeset
347 <has_text text=" pc " />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
parents:
diff changeset
348 <has_text text=" sc " />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
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diff changeset
349 </assert_command>
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
parents:
diff changeset
350 </test>
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
parents:
diff changeset
351 <!-- test with MS/MS input and other non-default values
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
parents:
diff changeset
352 (creates empty output .. but test is still usefull) -->
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
parents:
diff changeset
353 <test expect_num_outputs="1">
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
parents:
diff changeset
354 <param name="ms" ftype="tabular" value="CreatineMs.txt" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
parents:
diff changeset
355 <param name="msms" ftype="tabular" value="CreatineMsMs.txt" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
parents:
diff changeset
356 <conditional name="formula_cond">
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
parents:
diff changeset
357 <param name="formula_select" value=""/>
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
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diff changeset
358 </conditional>
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
parents:
diff changeset
359 <param name="m" value="111.0201" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
parents:
diff changeset
360 <param name="ion" value="M-H" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
parents:
diff changeset
361 <param name="ppm" value="4" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
parents:
diff changeset
362 <param name="msmv" value="msmv=ndp"/>
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
parents:
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363 <param name="acc" value="21" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
parents:
diff changeset
364 <param name="rej" value="39" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
parents:
diff changeset
365 <param name="thms" value="0.3" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
parents:
diff changeset
366 <param name="thmsms" value="0.2" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
parents:
diff changeset
367 <param name="thcomb" value="0.1" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
parents:
diff changeset
368 <param name="sort" value="sort=combmv" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
parents:
diff changeset
369 <conditional name="elemfilt_cond">
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
parents:
diff changeset
370 <param name="elemfilt_select" value="elem"/>
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
parents:
diff changeset
371 <param name="el" value="C,N,O,P,S,H,Cl,Br,F,I" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
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372 </conditional>
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
parents:
diff changeset
373 <param name="het" value="het" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
parents:
diff changeset
374 <param name="hcf" value="hcf" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
parents:
diff changeset
375 <param name="wm" value="wm=sqrt"/>
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
parents:
diff changeset
376 <conditional name="wi_cond">
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
parents:
diff changeset
377 <param name="wi" value="wi=log"/>
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
parents:
diff changeset
378 <param name="exp" value="2.31"/>
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
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diff changeset
379 </conditional>
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
parents:
diff changeset
380 <param name="oei" value="oei" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
parents:
diff changeset
381 <param name="dbeexc" value="1" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
parents:
diff changeset
382 <output name="out" ftype="tabular" file="CreatineMsMs.out" lines_diff="3"/>
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
parents:
diff changeset
383 <assert_command>
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
parents:
diff changeset
384 <has_text text=" ms=" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
parents:
diff changeset
385 <has_text text=" msms=" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
parents:
diff changeset
386 <not_has_text text=" exist" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
parents:
diff changeset
387 <has_text text=" m=111.0201" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
parents:
diff changeset
388 <has_text text=" ion=M-H" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
parents:
diff changeset
389 <has_text text=" ppm=4" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
parents:
diff changeset
390 <has_text text=" msmv=ndp" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
parents:
diff changeset
391 <has_text text=" acc=21" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
parents:
diff changeset
392 <has_text text=" rej=39" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
parents:
diff changeset
393 <has_text text=" thms=0.3" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
parents:
diff changeset
394 <has_text text=" thmsms=0.2" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
parents:
diff changeset
395 <has_text text=" thcomb=0.1" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
parents:
diff changeset
396 <has_text text=" sort=combmv" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
parents:
diff changeset
397 <has_text text=" el=CNOPSHClBrFI" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
parents:
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398 <not_has_text text=" oc " />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
parents:
diff changeset
399 <not_has_text text=" ff=" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
parents:
diff changeset
400 <has_text text=" het " />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
parents:
diff changeset
401 <not_has_text text=" vsp=" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
parents:
diff changeset
402 <not_has_text text=" vsp2mv=" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
parents:
diff changeset
403 <not_has_text text=" vsm2ap2=" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
parents:
diff changeset
404 <has_text text=" hcf " />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
parents:
diff changeset
405 <has_text text=" wm=sqrt " />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
parents:
diff changeset
406 <has_text text=" wi=log " />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
parents:
diff changeset
407 <has_text text=" exp=2.31 " />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
parents:
diff changeset
408 <has_text text=" oei " />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
parents:
diff changeset
409 <has_text text=" dbeexc=1" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
parents:
diff changeset
410 <not_has_text text=" ivsm2mv=" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
parents:
diff changeset
411 <not_has_text text=" ivsm2ap2=" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
parents:
diff changeset
412 <not_has_text text=" oms=" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
parents:
diff changeset
413 <not_has_text text=" omsms=" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
parents:
diff changeset
414 <not_has_text text=" oclean=" />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
parents:
diff changeset
415 <not_has_text text=" analyze " />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
parents:
diff changeset
416 <not_has_text text=" loss " />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
parents:
diff changeset
417 <not_has_text text=" intens " />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
parents:
diff changeset
418 <not_has_text text=" dbe " />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
parents:
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419 <not_has_text text=" cm " />
f17273aa599f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ commit 479866669d9dcf8f89140c68f701db1cd12b006e-dirty
matthias
parents:
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420 <not_has_text text=" pc " />
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421 <not_has_text text=" sc " />
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422 </assert_command>
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423 </test>
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424 </tests>
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425 <help><![CDATA[
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426
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427 **Overview**
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428
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429 The computer program genform generates candidate molecular formulas from high-resolution
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430 MS data. It calculates match values (MV) that show how well candidate molecular formulas fit the MS
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431 isotope peak distributions (MS MV) and the high-resolution MS/MS fragment peak masses (MSMS
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432 MV). Finally it computes a combined match value from these two scores. This software can be
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433 regarded as a further development of the ElCoCo and MolForm modules of MOLGEN-MS with a clear
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434 specialization towards MS/MS.
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435
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436 **Input**
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437
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438 MS and MS/MS centroided spectra are given as tab separated files with two columns:
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439
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440 1. m/z
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441 2. intensity
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442
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443 **Output**
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444
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445 Main output containing a list of all possible molecular formulas, further options can be chosen:
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446
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447 1. if the explained peaks shall also be written to the output
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448 2. if the explanation shall be given as molecular formulas for the fragment or as neutral losses
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449 3. double bond equivalents for each molecular formula
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450 4. calculated ion masses
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451 5. output match values in percent
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452
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453 Output structure:
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454
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455 molecular fomula / (double bond equivalent) / (calculated mass) / ppm / MS MV / MSMS MV / combined MV
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456
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457 ppm: The value ppm denotes the relative deviation of
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458 the calculated mass of the molecular ion from the mass of the basepeak (basemass) in the MS in
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459 parts per million (ppm).
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460
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461 MS MV: It is calculated from measured and
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462 theoretical isotope peak intensities. The MV ranges from 0 to 1. The better theoretical and measured
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463 isotope distributions fit, the higher is the MV. There are three different algorithms implemented for
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464 calculating the MS MV, which are nomalized dot product, nomalized sum of squared errors and the normalized sum of absolute errors.
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465
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466 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
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467 between 0 and 1, whereby higher values reflect a better fit.
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468
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469 combined MV: combined match value
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470
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471 Example output:
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472
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473 ======== === =========== ====== ======== ========= ========
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474 C4H9N3O2 2 132.07675 -0.8 96.674 100.000 96.674
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475 ======== === =========== ====== ======== ========= ========
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476
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477 **Advanced options**
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478
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479 ...
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480
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481 ]]></help>
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482
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483 <citations>
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484 <citation type="doi">10.3390/metabo3020440</citation>
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485 <citation type="bibtex">@article{meringer2011ms,
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486 title={MS/MS data improves automated determination of molecular formulas by mass spectrometry},
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487 author={Meringer, Markus and Reinker, Stefan and Zhang, Juan and Muller, Alban},
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488 journal={MATCH Commun. Math. Comput. Chem},
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489 volume={65},
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490 number={2},
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491 pages={259--290},
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492 year={2011}
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493 }</citation>
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494 </citations>
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495 </tool>