Mercurial > repos > gmat > isocor
comparison isocor.xml @ 1:fa183805db31 draft default tip
"planemo upload"
| author | gmat |
|---|---|
| date | Mon, 04 May 2020 11:38:09 -0400 |
| parents | 96f7617b4848 |
| children |
comparison
equal
deleted
inserted
replaced
| 0:96f7617b4848 | 1:fa183805db31 |
|---|---|
| 1 <tool id="isocor" name="Isotope Correction for mass spectrometry labeling experiments" version="0.1.2"> | 1 <tool id="isocor" name="Isotope Correction for mass spectrometry labeling experiments" version="0.1.3"> |
| 2 <requirements> | 2 <requirements> |
| 3 <requirement type="package" version="2.1.3">isocor</requirement> | 3 <requirement type="package" version="2.2.0">isocor</requirement> |
| 4 </requirements> | 4 </requirements> |
| 5 <command detect_errors="exit_code"><![CDATA[ | 5 <command detect_errors="exit_code"><![CDATA[ |
| 6 isocorcli -t "$tracer" -M "$input1" -D "$input2" -I "$input3" | 6 isocorcli -t "$tracer" -M "$db.input1" -D "$db.input2" -I "$db.input3" |
| 7 #if $tracer_purity: | 7 #if $tcorrection.tracer_purity: |
| 8 -p $tracer_purity | 8 -p $tcorrection.tracer_purity |
| 9 #end if | 9 #end if |
| 10 #if $resolution: | 10 #if $HR.resolution: |
| 11 -r $resolution | 11 -r $HR.resolution |
| 12 #end if | 12 #end if |
| 13 #if $mz: | 13 #if $HR.mz: |
| 14 -m $mz | 14 -m $HR.mz |
| 15 #end if | 15 #end if |
| 16 #if $resolution_formula_code: | 16 #if $HR.resolution_formula_code: |
| 17 -f $resolution_formula_code | 17 -f $HR.resolution_formula_code |
| 18 #end if | 18 #end if |
| 19 #if $correct_na_tracer: | 19 #if $tcorrection.correct_na_tracer: |
| 20 -n | 20 -n |
| 21 #end if | 21 #end if |
| 22 #if $verbose_log: | 22 #if $verbose_log: |
| 23 -v | 23 -v |
| 24 #end if | 24 #end if |
| 25 "$input4" > "$output1" 2> "$output2" | 25 "$input4" > "$output1" 2> "$output2" |
| 26 ]]></command> | 26 ]]></command> |
| 27 <inputs> | 27 <inputs> |
| 28 <param type="text" name="tracer" argument="-t" label="the isotopic tracer (e.g. '13C')" /> | 28 <param type="text" name="tracer" argument="-t" label="the isotopic tracer (e.g. '13C')" /> |
| 29 <param type="data" name="input1" argument="-M" label="metabolites db" format="tabular" /> | 29 <param type="data" name="input4" label="measurements Data file" format="tabular" help="This file contains the raw MS data for each metabolite of each sample." /> |
| 30 <param type="data" name="input2" argument="-D" label="derivatives db" format="tabular" /> | 30 <section name="db" title="Database Files" expanded="true" help="The exact mass and natural abundance of each isotope and the elemental formulas used for correction have to be defined carefully, otherwise the correction will be wrong. IsoCor rely on several flat-files to store this information. Pre-configured files are shipped with IsoCor. For a good start download them on github"> |
| 31 <param type="data" name="input3" argument="-I" label="isotopes db" format="csv" /> | 31 <param type="data" name="input1" argument="-M" label="metabolites db" format="tabular" /> |
| 32 <param type="integer" optional="true" argument="-r" name="resolution" label="HR only: resolution of the mass spectrometer (e.g. 1e4)" /> | 32 <param type="data" name="input2" argument="-D" label="derivatives db" format="tabular" /> |
| 33 <param type="integer" optional="true" argument="-m" name="mz" label="HR only: mz at which resolution is given (e.g. '400')" /> | 33 <param type="data" name="input3" argument="-I" label="isotopes db" format="csv" /> |
| 34 <param type="boolean" optional="true" argument="-n" name="correct_na_tracer" label="flag to correct tracer natural abundance" /> | 34 </section> |
| 35 <param type="boolean" optional="true" argument="-v" name="verbose_log" label="flag to enable verbose logs" /> | 35 <section name="HR" title="High Resolution Parameters" expanded="true" help="For measurements collected at high or ultrahigh resolution (e.g. on Orbitrap or FT-ICR instruments). Measurements collected at unitary resolution (e.g. on quadrupole instruments) are Low Resolution, don't fill this section."> |
| 36 <param type="text" optional="true" argument="-p" name="tracer_purity" label="purity vector of the tracer" /> | 36 <param name="resolution_formula_code" optional="true" argument="-f" type="select" label="HR only: spectrometer formula code"> |
| 37 <option value="orbitrap">Orbitrap</option> | |
| 38 <option value="ft-icr">ft-icr</option> | |
| 39 <option value="constant">Constant</option> | |
| 40 <option value="datafile">Datafile</option> | |
| 41 </param> | |
| 42 <param type="integer" optional="true" argument="-r" name="resolution" label="HR only: resolution of the mass spectrometer (e.g. '60000' or '1e4')" /> | |
| 43 <param type="integer" optional="true" argument="-m" name="mz" label="HR only: mz at which resolution is given (e.g. '400')" /> | |
| 44 </section> | |
| 45 <section name="tcorrection" title="Tracer Correction Options" expanded="true"> | |
| 46 <param type="boolean" optional="true" argument="-n" name="correct_na_tracer" label="flag to correct tracer natural abundance" help="Correct for the contribution of naturally occurring isotopes of the tracer element at unlabeled positions. This only concerns the tracer element: natural abundance of other elements is always corrected." /> | |
| 47 <param type="text" optional="true" argument="-p" name="tracer_purity" label="purity vector of the tracer (e.g. '0,0,0.99,0.01')" help="Correct for the contribution of isotopic impurities of the tracer at labeled positions. The isotopic purity is typically obtained from the manufacturer. e.g. ¹³C-substates with purity of 99%, use 0.01 for ¹²C and 0.99 for ¹³C." /> | |
| 48 </section> | |
| 49 <param type="boolean" optional="true" argument="-v" name="verbose_log" label="flag to enable verbose logs" help="Useful in case of trouble. Join it to the issue on github." /> | |
| 37 | 50 |
| 38 <param name="resolution_formula_code" optional="true" argument="-f" type="select" label="HR only: spectrometer formula code"> | |
| 39 <option value="orbitrap">Orbitrap</option> | |
| 40 <option value="ft-icr">ft-icr</option> | |
| 41 <option value="constant">Constant</option> | |
| 42 <option value="datafile">Datafile</option> | |
| 43 </param> | |
| 44 | 51 |
| 45 <param type="data" name="input4" label="measurements Data file" format="tabular" /> | |
| 46 </inputs> | 52 </inputs> |
| 47 <outputs> | 53 <outputs> |
| 48 <data name="output1" label="corrected measurements data file" format="csv" /> | 54 <data name="output1" label="corrected measurements data file" format="tabular" /> |
| 49 <data name="output2" label="processing log file" format="txt" /> | 55 <data name="output2" label="processing log file" format="txt" /> |
| 50 </outputs> | 56 </outputs> |
| 51 <tests> | 57 <tests> |
| 52 <test> | 58 <test> |
| 53 <param name="tracer" value="13C"/> | 59 <param name="tracer" value="13C"/> |
| 54 <param name="input1" value="Metabolites.dat"/> | 60 <section name="db"> |
| 55 <param name="input2" value="Derivatives.dat"/> | 61 <param name="input1" value="Metabolites.dat"/> |
| 56 <param name="input3" value="Isotopes.dat"/> | 62 <param name="input2" value="Derivatives.dat"/> |
| 63 <param name="input3" value="Isotopes.dat"/> | |
| 64 </section> | |
| 57 <param name="input4" value="Data_example.tsv"/> | 65 <param name="input4" value="Data_example.tsv"/> |
| 58 <output name="output1"> | 66 <output name="output1"> |
| 59 <assert_contents> | 67 <assert_contents> |
| 60 <has_n_columns n="9" /> | 68 <has_n_columns n="10" /> |
| 61 </assert_contents> | 69 </assert_contents> |
| 62 </output> | 70 </output> |
| 63 <output name="output2"> | 71 <output name="output2"> |
| 64 <assert_contents> | 72 <assert_contents> |
| 65 <has_text text="- root - INFO - errors: 0" /> | 73 <has_text text="- root - INFO - errors: 0" /> |
| 66 </assert_contents> | 74 </assert_contents> |
| 67 </output> | 75 </output> |
| 76 </test> | |
| 77 <test> | |
| 78 <param name="tracer" value="13C"/> | |
| 79 <section name="db"> | |
| 80 <param name="input1" value="Metabolites.dat"/> | |
| 81 <param name="input2" value="Derivatives.dat"/> | |
| 82 <param name="input3" value="Isotopes.dat"/> | |
| 83 </section> | |
| 84 <section name="HR"> | |
| 85 <param name="mz" value="400"/> | |
| 86 <param name="resolution" value="60000"/> | |
| 87 <param name="resolution_formula_code" value="orbitrap"/> | |
| 88 </section> | |
| 89 <section name="tcorrection"> | |
| 90 <param name="correct_na_tracer" value="-n"/> | |
| 91 <param name="tracer_purity" value="0.01,0.99"/> | |
| 92 </section> | |
| 93 <param name="input4" value="Data_example.tsv"/> | |
| 94 <output name="output1"> | |
| 95 <assert_contents> | |
| 96 <has_n_columns n="10" /> | |
| 97 </assert_contents> | |
| 98 </output> | |
| 99 <output name="output2"> | |
| 100 <assert_contents> | |
| 101 <has_text text="- root - INFO - errors: 0" /> | |
| 102 </assert_contents> | |
| 103 </output> | |
| 68 </test> | 104 </test> |
| 69 </tests> | 105 </tests> |
| 70 <help><![CDATA[ | 106 <help><![CDATA[ |
| 71 .. class:: warningmark | 107 .. class:: warningmark |
| 72 | 108 |