changeset 0:4f0efe305bff draft default tip

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantwiz_iq commit 7e54991bc641a1f70855b686c987f3f331142db1"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/quantwiz_iq.xml	Tue Jan 21 15:21:38 2020 -0500
@@ -0,0 +1,189 @@
+<tool id="quantwiz_iq" name="QuantWiz-IQ" version="2.0">
+    <description>Isobaric Quantitation using QuantWiz-IQ</description>
+    <requirements>
+        <requirement type="package" version="2.0">quantwiz-iq</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+cp '$input_file' '$input_file.name'
+&&
+cat '$new_param_file' > '$iq_params'
+#if $input_purity_file.input_purity_file_option == "history":
+    && cp '$input_purity_file.purity_type' '$input_purity_file.purity_type.name'
+    && echo "Purity_corrections_values=$input_purity_file.purity_type.name" >> '$iq_params'
+#else:
+    && PROG_PATH=`which QuantWiz_IQ`
+    && cp \${PROG_PATH%/*}/Purity_correction/$input_purity_file.purity_type .
+    && echo "Purity_corrections_values=$input_purity_file.purity_type" >> '$iq_params'
+#end if
+
+&&
+QuantWiz_IQ '$iq_params'
+&& cp '${input_file.name.rsplit('.',1)[0]}_${area_method}_${min_tol}.tsv' '$quant'
+&& cp '${input_file.name.rsplit('.',1)[0]}_${area_method}_${min_tol}_noquant.tsv' '$noquant'
+    ]]>
+    </command>
+    <configfiles>
+        <configfile name="new_param_file"><![CDATA[#slurp
+Spectra_Folder=.
+#if $input_file.ext == "mgf":
+Input_file_extension=mgf
+#else if $input_file.ext == "mzml":
+Input_file_extension=mzML
+#end if
+Label_type=$input_label.label_type
+Plex=$input_label.num_plex
+min_reporters=$min_reporters
+Spectrum_area=$area_method
+Base_reporter=$input_label.base_reporter
+Normalization=$normalization
+Peak_intensity_threshold=$peak_intensity_threshold
+Tol_unit=$tol_unit
+Tol_min=$min_tol
+Tol_max=$max_tol
+#slurp
+]]></configfile>
+    </configfiles>
+    
+    <inputs>
+        <param type="data" name="input_file" format="mgf,mzml" label="MGF/mzML file"/>
+        
+        <conditional name="input_label">
+            <param name="label_type" type="select" label="Isobaric reporter labeling type (MS2 level): iTRAQ or TMT">
+                <option value="iTRAQ" selected="true">iTRAQ</option>
+                <option value="TMT">TMT</option>
+            </param>
+            <when value="iTRAQ">
+                <param name="num_plex" type="select" display="radio" label="You are using iTRAQ: 4Plex or 8Plex">
+                    <option value="4plex" selected="true">4Plex</option>
+                    <option value="8plex">8Plex</option>
+                </param>
+                <param name="base_reporter" type="select" label="Denominator reporter tag for ratio calculation (mention only base reporter integer value)">
+                    <option value="113" selected="true">113</option>
+                    <option value="114">114</option>
+                    <option value="115">115</option>
+                    <option value="116">116</option>
+                    <option value="117">117</option>
+                    <option value="118">118</option>
+                    <option value="119">119</option>
+                    <option value="121">121</option>
+                </param>
+            </when> 
+            <when value="TMT">
+                <param name="num_plex" type="select" display="radio" label="You are using TMT: 2Plex, 6Plex or 10Plex">
+                    <option value="2plex">2Plex</option>
+                    <option value="6plex">6Plex</option>
+                    <option value="10plex" selected="true">10Plex</option>
+                </param>
+                <param name="base_reporter" type="select" label="Denominator reporter tag for ratio calculation (mention only base reporter integer value)">
+                    <option value="126" selected="true">126</option>
+                    <option value="127">127</option>
+                    <option value="128">128</option>
+                    <option value="129">129</option>
+                    <option value="130">130</option>
+                    <option value="131">131</option>
+                </param>
+            </when>
+        </conditional>
+        
+        <param name="min_reporters" type="integer" value="2" min="0" label="Minimum number of reporter types required to consider a spectrum for quantitation. Default is 2" />
+        
+        <param name="area_method" type="select" label="Spectrum area calculation method">
+            <option value="T">Trapezoid</option>
+            <option value="S" selected="true">Sum intensity</option>
+            <option value="B">Baseline corrected sum intensity</option>
+        </param>
+        
+        <param name="normalization" type="select" display="radio" label="Perform normalization">
+            <option value="yes">Yes</option>
+            <option value="no" selected="true">No</option>
+        </param>
+        
+        <param name="peak_intensity_threshold" type="float" value="0.0" min="0.0" label="Reporter label maximum peak intensity threshold" help="Reporter label maximum peak intensity threshold to consider the tag for quantitation. Default is 0. It depends on signal to noise ratio (S/N)" />
+        
+        <param name="tol_unit" type="select" display="radio" label="MS/MS (MS2) tolerance unit">
+            <option value="Da" selected="true">Dalton (Da)</option>
+            <option value="ppm">Parts per million (ppm)</option>
+        </param>
+        
+        <param name="min_tol" type="float" value="0.05" min="0.0" label="Minimum MS/MS (MS2) tolerance range" />
+        <param name="max_tol" type="float" value="0.05" min="0.0" label="Maximum MS/MS (MS2) tolerance range" />
+        
+        <conditional name="input_purity_file">
+            <param name="input_purity_file_option" type="select" display="radio" label="Use default or from the history">
+                <option value="default" selected="true">Use Default</option>
+                <option value="history">Use file from the history</option>
+            </param>
+            <when value="default">
+                <param name="purity_type" type="select" label="Select default purity correction type">
+                    <option value="iTRAQ4plex.tsv">iTRAQ 4plex</option>
+                    <option value="iTRAQ8plex.tsv" selected="true">iTRAQ 8plex</option>
+                    <option value="TMT6plex.tsv">TMT 6plex</option>
+                    <option value="TMT10plex.tsv">TMT 10plex</option>
+                </param>
+            </when> 
+            <when value="history">
+                <param type="data" name="purity_type" format="txt" label="Select purity correction file from the history"/>
+            </when> 
+        </conditional>
+    </inputs>
+    
+    <outputs>
+        <data name="quant" format="tabular" label="${tool.name}_Quant.tabular" from_work_dir="${input_file.name.rsplit('.',1)[0]}_${area_method}_${min_tol}.tsv"/>
+        <data name="noquant" format="tabular" label="${tool.name}_No_Quant.tabular" from_work_dir="${input_file.name.rsplit('.',1)[0]}_${area_method}_${min_tol}_noquant.tsv"/>
+        <data name="iq_params" format="txt" label="${tool.name}_QuantWiz_IQ_parameters"/>
+    </outputs>
+    
+    <tests>
+        <test>
+            <param name="input_file" value="Test_Orbi_iTRAQ_8plex.mgf" ftype="mgf"/>
+            <param name="label_type" value="iTRAQ"/>
+            <param name="num_plex" value="8plex"/>
+            <param name="min_reporters" value="1"/>
+            <param name="area_method" value="S"/>
+            <param name="base_reporter" value="113"/>
+            <param name="normalization" value="no"/>
+            <param name="peak_intensity_threshold" value="0.0"/>
+            <param name="tol_unit" value="Da"/>
+            <param name="min_tol" value="0.05"/>
+            <param name="max_tol" value="0.05"/>
+            <param name="input_purity_file_option" value="default"/>
+            <param name="purity_type" value="iTRAQ8plex.tsv"/>
+            <output name="quant" file="Test_Orbi_iTRAQ_8plex_S_0.05.tsv">
+                <assert_contents>
+                    <has_text text="Retention_time"/>
+                </assert_contents>
+            </output>
+            <output name="noquant" file="Test_Orbi_iTRAQ_8plex_S_0.05_noquant.tsv">
+                <assert_contents>
+                    <has_text text="Base_Intensity"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    
+    <help><![CDATA[
+
+**QuantWiz-IQ** for Isobaric Quantitation
+        
+IQ stands for Isobaric Quantitator, a tool for quantitation based on of Isobaric tags (iTRAQ and TMT) that takes
+MGF as well as the HUPO-PSI standard mzML as input. It supports 4-plex and 8-plex quantitation for iTRAQ;
+and 2-plex, 6-plex and 10-plex quantitation for TMT.
+
+**Outputs**:
+
+Outputs parameters file along with two tabular files. One tabular file contains spectra that shows quantitation,
+and the other tabular file with spectra that didn't show any qualified quantitation.
+        
+    ]]></help>
+    
+    <citations>
+        <citation type="bibtex">
+            @misc{quantwiz_iq,
+            author={Aggarwal, Suruchi and Yadav, Amit Kumar and Kumar, Praveen},
+            year={2020},
+            title={QuantWiz-IQ Galaxy Wrapper}
+            }
+        </citation>
+        <citation type="doi">10.1007/978-1-4939-3106-4_18</citation>
+    </citations>
+</tool>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Test_Orbi_iTRAQ_8plex.mgf	Tue Jan 21 15:21:38 2020 -0500
@@ -0,0 +1,5056 @@
+BEGIN IONS
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+END IONS

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Test_Orbi_iTRAQ_8plex_S_0.05.tsv	Tue Jan 21 15:21:38 2020 -0500
@@ -0,0 +1,5 @@
+Scan	Title	Retention_time	Base_Intensity	PEPMASS	Charge	MSLevel	Previous Scan	113/113.1078734	114/113.1078734	115/113.1078734	116/113.1078734	117/113.1078734	118/113.1078734	119/113.1078734	121/113.1078734	113/113.1078734-Err	114/113.1078734-Err	115/113.1078734-Err	116/113.1078734-Err	117/113.1078734-Err	118/113.1078734-Err	119/113.1078734-Err	121/113.1078734-Err	113_Peak_Max	114_Peak_Max	115_Peak_Max	116_Peak_Max	117_Peak_Max	118_Peak_Max	119_Peak_Max	121_Peak_Max	113_Area	114_Area	115_Area	116_Area	117_Area	118_Area	119_Area	121_Area	113_Error	114_Error	115_Error	116_Error	117_Error	118_Error	119_Error	121_Error
+6	Orbi - HCD_100msNCE50_4fr-hela-halvan_0-5of25ul.7.7.3	2.5545	250117.890625	541.633728027344	3+	NA	NA	1	0.97293686985836	0.345480025116026	0.439590611285727	0.955409517577147	0.924897100616241	0.464434486191085	0.420023626761269	0.805065081542481	0.813484055143247	1.1993257654087	1.0698352974366	0.816625040319075	0.830352966972191	1.02771360778193	1.044923050208	28068.443359375	27686.986328125	11519.69921875	13732.59375	27103.22265625	27074.900390625	13678.0341796875	11732.2548828125	29430.1971613561	28633.7239054842	10167.5452544749	12937.23836042	28117.8904721316	27219.9040251026	13668.3984971368	12361.378148012	167.536394133857	166.394069389882	107.329861728924	117.186149992224	164.630564161853	164.544524037189	116.953128131262	108.315533894324
+7	Orbi - HCD_100msNCE50_4fr-hela-halvan_0-5of25ul.8.8.3	2.9349	72122.6796875	678.715515136719	3+	NA	NA	1	1.05344283511644	0.364151199900742	0.496087204978236	0.848544445986835	0.96467674163776	0.522524472159182	0.482326477430071	1.5706922662197	1.55453754968185	2.29734932798631	1.98543906905228	1.64787947865785	1.59997866740934	1.92266681091877	1.94329755394583	7386.3686523438	7861.4702148438	3211.3166503906	3991.2839355469	6389.505859375	7391.203125	4026.947265625	3542.2958984375	7738.18987870642	8151.74068449386	2817.87112939072	3838.81698851835	6566.19804356788	7464.85179836481	4043.3935818386	3732.3338658815	85.9439855507283	88.6649322722563	56.6684802195241	63.1766090855381	79.9343847125566	85.972106668384	63.4582324495806	59.5171899407012
+8	Orbi - HCD_100msNCE50_4fr-hela-halvan_0-5of25ul.9.9.4	3.576	70229.03125	576.321655273438	4+	NA	NA	1	1.1154204768379	0.300334759379282	0.525755206494072	0.965911621689543	1.14599573551886	0.614028894665772	0.327438171423764	2.0406007302296	1.99012113757338	3.28633841144885	2.52524543397221	2.06783151833036	1.99061997453009	2.37026004803342	2.89920920422462	4381.8842773438	4918.994140625	1655.017578125	2498.5546875	4307.9111328125	5197.8520507813	2805.9365234375	1426.8663330078	4587.61973246654	5117.12498953878	1377.82166847398	2411.96495975922	4431.2352154817	5257.39264958884	2816.93107347331	1502.16181638642	66.1958025659014	70.1355412086126	40.681907257711	49.9855447854677	65.6346793456973	72.0961306228101	52.9710913936791	37.7738842721767
+9	Orbi - HCD_100msNCE50_4fr-hela-halvan_0-5of25ul.10.10.3	4.1116	53250.47265625	496.281372070313	3+	NA	NA	1	0.975441784238905	0.452481797184021	0.429902374249284	0.861215148378896	0.878206889821254	0.517208020110321	0.388198687752429	1.83703381345298	1.85604017449991	2.43331455780748	2.46764140846258	1.91671219527066	1.92118897105817	2.25352546090581	2.45230487735302	5390.9936523438	5342.8388671875	2769.3896484375	2599.232421875	4707.2045898438	4937.1196289063	2898.1889648438	2083.0734863281	5652.391801801	5513.57914436612	2557.60440086714	2429.97665578144	4867.9254442837	4963.96942431081	2923.4623726973	2194.25108012173	73.4233862767429	73.0947253034547	52.6249907214956	50.982667857567	68.6090707548484	70.264639961408	53.8348304060095	45.640699888675

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Test_Orbi_iTRAQ_8plex_S_0.05_noquant.tsv	Tue Jan 21 15:21:38 2020 -0500
@@ -0,0 +1,9 @@
+Scan	Title	Retention_time	Base_Intensity	PEPMASS	Charge	MSLevel	Previous Scan
+1	Orbi - HCD_100msNCE50_4fr-hela-halvan_0-5of25ul.2.2.3	0.8306	250117.890625	541.633728027344	3+
+2	Orbi - HCD_100msNCE50_4fr-hela-halvan_0-5of25ul.3.3.3	1.0229	72122.6796875	678.715515136719	3+
+3	Orbi - HCD_100msNCE50_4fr-hela-halvan_0-5of25ul.4.4.4	1.3423	70229.03125	576.321655273438	4+
+4	Orbi - HCD_100msNCE50_4fr-hela-halvan_0-5of25ul.5.5.3	1.6044	53250.47265625	496.281372070313	3+
+5	Orbi - HCD_100msNCE50_4fr-hela-halvan_0-5of25ul.6.6.4	1.9293	63023.37109375	909.705139160156	4+
+10	Orbi - HCD_100msNCE50_4fr-hela-halvan_0-5of25ul.11.11.4	4.7926	63023.37109375	909.705139160156	4+
+11	Orbi - HCD_100msNCE50_4fr-hela-halvan_0-5of25ul.13.13.4	6.2091	69842.609375	576.7978515625	4+
+12	Orbi - HCD_100msNCE50_4fr-hela-halvan_0-5of25ul.14.14.3	6.467	35365.69140625	490.605255126953	3+