Repository 'msstatstmt'
hg clone https://toolshed.g2.bx.psu.edu/repos/galaxyp/msstatstmt

Changeset 2:782bd55b000b (2021-02-27)
Previous changeset 1:b79d4c961009 (2021-02-05) Next changeset 3:5667ff6f7a40 (2021-03-12)
Commit message:
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 1272b32052ad8b986c1d3bd14f7cb9e3e921c74f"
modified:
msstatstmt.xml
test-data/ProfilePlot.pdf
test-data/ProfilePlot_list.pdf
test-data/QCPlot.pdf
added:
test-data/MSstats_group_ComparisonPlot.pdf
test-data/MSstats_group_Heatmap.pdf
test-data/MSstats_group_VolcanoPlot.pdf
test-data/annotation.pd.txt
test-data/input.pd.txt
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diff -r b79d4c961009 -r 782bd55b000b msstatstmt.xml
--- a/msstatstmt.xml Fri Feb 05 18:42:55 2021 +0000
+++ b/msstatstmt.xml Sat Feb 27 10:54:25 2021 +0000
[
b'@@ -1,8 +1,8 @@\n <tool id="msstatstmt" name="MSstatsTMT" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">\n     <description>protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling</description>\n     <macros>\n-        <token name="@TOOL_VERSION@">1.8.0</token>\n-        <token name="@GALAXY_VERSION@">0</token>\n+        <token name="@TOOL_VERSION@">1.8.2</token>\n+        <token name="@GALAXY_VERSION@">1</token>\n         <xml name="input_options_shared">\n             <param name="useUniquePeptide" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Use unique peptide" help="Yes (default) removes peptides that are assigned for more than one protein. We assume to use unique peptide for each protein." />\n             <param name="rmPSM_withMissing_withinRun" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Remove PSM with missing value within run" help="Yes will remove PSM with any missing value within each run. Default is No." />\n@@ -22,6 +22,7 @@\n     <configfiles>\n         <configfile name="msstatstmt_script"><![CDATA[\n library(MSstatsTMT, warn.conflicts = F, quietly = T, verbose = F)\n+library(MSstats)\n \n #if $input.input_src == \'MSstatsTMT\'\n     input <- read.table("$input.msstatstmt_input", sep="\\t", header=TRUE)\n@@ -51,6 +52,21 @@\n                                       rmPSM_withfewMea_withinRun = $input.input_options.rmPSM_withfewMea_withinRun,\n                                       rmProtein_with1Feature = $input.input_options.rmProtein_with1Feature,\n                                       summaryforMultiplePSMs = $input.input_options.summaryforMultiplePSMs)\n+\n+#elif $input.input_src == \'PD\'\n+    PSM.pd <- read.table("$input.PSM", sep="\\t", header=TRUE)\n+    annotation.pd <- read.table("$input.annotation", sep="\\t", header=TRUE)\n+\n+    input <- PDtoMSstatsTMTFormat(PSM.pd,\n+                                  annotation = annotation.pd,\n+                                  which.proteinid = "$input.proteinID",\n+                                  useNumProteinsColumn = $input.input_options.useNumProteinsColumn,\n+                                  useUniquePeptide = $input.input_options.useUniquePeptide,\n+                                  rmPSM_withMissing_withinRun = $input.input_options.rmPSM_withMissing_withinRun,\n+                                  rmPSM_withfewMea_withinRun = $input.input_options.rmPSM_withfewMea_withinRun,\n+                                  rmProtein_with1Feature = $input.input_options.rmProtein_with1Feature,\n+                                  summaryforMultipleRows = $input.input_options.summaryforMultipleRows)\n+\n #end if\n \n quant <- proteinSummarization(input,\n@@ -71,15 +87,15 @@\n         dataProcessPlotsTMT(input,\n                             quant,\n                             type = \'$plot_type\',\n-                            ylimUp = $out_plots_opt.ylimUp,\n-                            ylimDown = $out_plots_opt.ylimDown,\n-                            x.axis.size = $out_plots_opt.x_axis_size,\n-                            y.axis.size = $out_plots_opt.y_axis_size,\n-                            text.size = $out_plots_opt.text_size,\n-                            text.angle = $out_plots_opt.text_angle,\n-                            legend.size = $out_plots_opt.legend_size,\n-                            dot.size.profile = $out_plots_opt.dot_size_profile,\n-                            ncol.guide = $out_plots_opt.ncol_guide,\n+                            ylimUp = $out_plots_opt.adv.ylimUp,\n+                            ylimDown = $out_plots_opt.adv.ylimDown,\n+                            x.axis.size = $out_plots_opt.adv.x_axis_size,\n+                            y.axis.size = $out_plots_opt.adv.y_axis_size,\n+                            text.size = $out_plots_opt.adv.text_size,\n+                            text.angle = $out_plots_opt.adv.text_angle,\n+                            legend.size = $out_plots_opt.adv.legend'..b'\'group_comparison\'] == \'true\' and \'Heatmap\' in group[\'selected_group_outputs\']</filter>\n+        </data>\n+        <data name="out_group_comp_plot" from_work_dir="MSstats_group_ComparisonPlot.pdf" format="pdf" label="${tool.name} on ${on_string}: Group Comparison - Comparison Plot">\n+            <filter>group[\'group_comparison\'] == \'true\' and \'ComparisonPlot\' in group[\'selected_group_outputs\']</filter>\n         </data>\n     </outputs>\n     <tests>\n@@ -277,13 +429,13 @@\n             </output>\n             <output name="out_r_script">\n                 <assert_contents>\n-                    <has_n_lines n="51" />\n+                    <has_n_lines n="52" />\n                 </assert_contents>\n             </output>\n             <output name="out_profile_plot" file="ProfilePlot.pdf" compare="sim_size"/>\n             <output name="out_qc_plot" file="QCPlot.pdf" compare="sim_size"/>\n         </test>\n-        <test expect_num_outputs="2">\n+        <test expect_num_outputs="4">\n             <conditional name="input">\n                 <param name="input_src" value="MaxQuant"/>\n                 <param name="evidence" ftype="tabular" value="evidence.txt"/>\n@@ -296,6 +448,7 @@\n                     <param name="select" value="true"/>\n                     <param name="comparison_matrix" ftype="tabular" value="comparison_matrix.txt"/>\n                 </conditional>\n+                <param name="selected_group_outputs" value="comparison_result,VolcanoPlot,ComparisonPlot"/>\n             </conditional>\n             <param name="selected_outputs" value="ProfilePlot"/>\n             <conditional name="which_Protein">\n@@ -312,16 +465,24 @@\n                 </assert_contents>\n             </output>\n             <output name="out_profile_plot" file="ProfilePlot_list.pdf" compare="sim_size"/>\n+            <output name="out_group_volcano_plot" file="MSstats_group_VolcanoPlot.pdf" compare="sim_size"/>\n+            <output name="out_group_comp_plot" file="MSstats_group_ComparisonPlot.pdf" compare="sim_size"/>\n         </test>\n-        <test expect_num_outputs="2">\n+        <test expect_num_outputs="3">\n             <conditional name="input">\n                 <param name="input_src" value="OpenMS"/>\n                 <param name="oms_input" ftype="tabular" value="input.oms.txt"/>\n             </conditional>\n             <conditional name="group">\n                 <param name="group_comparison" value="true"/>\n+                <param name="selected_group_outputs" value="comparison_result,Heatmap"/>\n             </conditional>\n-            <param name="selected_outputs" value="msstats_log"/>\n+            <param name="selected_outputs" value="r_script"/>\n+            <output name="out_r_script">\n+                <assert_contents>\n+                    <has_n_lines n="58" />\n+                </assert_contents>\n+            </output>\n             <output name="out_group_comp">\n                 <assert_contents>\n                     <has_n_lines n="51" />\n@@ -330,6 +491,23 @@\n                     <has_text text="sp|O35226|PSMD4_MOUSE" />\n                 </assert_contents>\n             </output>\n+            <output name="out_group_heatmap" file="MSstats_group_Heatmap.pdf" compare="sim_size"/>\n+        </test>\n+        <test expect_num_outputs="1">\n+            <conditional name="input">\n+                <param name="input_src" value="PD"/>\n+                <param name="PSM" ftype="tabular" value="input.pd.txt"/>\n+                <param name="annotation" ftype="tabular" value="annotation.pd.txt"/>\n+            </conditional>\n+            <param name="selected_outputs" value="quant"/>\n+            <output name="out_quant">\n+                <assert_contents>\n+                    <has_n_lines n="1575" />\n+                    <has_n_columns n="8" />\n+                    <has_text text="PAMI-176_Mouse_A-J_1" />\n+                    <has_text text="Long_LF" />\n+                </assert_contents>\n+            </output>\n         </test>\n     </tests>\n     <help><![CDATA[\n'
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diff -r b79d4c961009 -r 782bd55b000b test-data/MSstats_group_ComparisonPlot.pdf
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diff -r b79d4c961009 -r 782bd55b000b test-data/MSstats_group_Heatmap.pdf
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diff -r b79d4c961009 -r 782bd55b000b test-data/MSstats_group_VolcanoPlot.pdf
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diff -r b79d4c961009 -r 782bd55b000b test-data/ProfilePlot.pdf
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diff -r b79d4c961009 -r 782bd55b000b test-data/ProfilePlot_list.pdf
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diff -r b79d4c961009 -r 782bd55b000b test-data/QCPlot.pdf
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diff -r b79d4c961009 -r 782bd55b000b test-data/annotation.pd.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/annotation.pd.txt Sat Feb 27 10:54:25 2021 +0000
b
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b
diff -r b79d4c961009 -r 782bd55b000b test-data/input.pd.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input.pd.txt Sat Feb 27 10:54:25 2021 +0000
[
b'@@ -0,0 +1,754 @@\n+"Checked"\t"Confidence"\t"Identifying Node"\t"PSM Ambiguity"\t"Annotated Sequence"\t"Modifications"\t"# Protein Groups"\t"# Proteins"\t"Master Protein Accessions"\t"Master Protein Descriptions"\t"Protein Accessions"\t"Protein Descriptions"\t"# Missed Cleavages"\t"Charge"\t"DeltaScore"\t"DeltaCn"\t"Rank"\t"Search Engine Rank"\t"m/z [Da]"\t"MH+ [Da]"\t"Theo. MH+ [Da]"\t"DeltaM [ppm]"\t"Deltam/z [Da]"\t"Activation Type"\t"MS Order"\t"Isolation Interference [%]"\t"Average Reporter S/N"\t"Ion Inject Time [ms]"\t"RT [min]"\t"First Scan"\t"Spectrum File"\t"File ID"\t"Abundance: 126"\t"Abundance: 127N"\t"Abundance: 127C"\t"Abundance: 128N"\t"Abundance: 128C"\t"Abundance: 129N"\t"Abundance: 129C"\t"Abundance: 130N"\t"Abundance: 130C"\t"Abundance: 131"\t"Quan Info"\t"Ions Score"\t"Identity Strict"\t"Identity Relaxed"\t"Expectation Value"\t"Percolator q-Value"\t"Percolator PEP"\r\n+"False"\t"High"\t"Mascot (A2)"\t"Unambiguous"\t"[K].aIDILDR.[SM]"\t"N-Term(TMT6plex)"\t"1"\t"1"\t""\t""\t"Q61084"\t"Mitogen-activated protein kinase kinase kinase 3 OS=Mus musculus GN=Map3k3 PE=1 SV=1"\t"0"\t"2"\t"0.0000"\t"0.0000"\t"1"\t"1"\t"522.81610"\t"1044.62493"\t"1044.62508"\t"-0.14"\t"-0.00008"\t"CID"\t"MS2"\t"2.279464"\t"10.5"\t"42.390"\t"63.4111"\t"16103"\t"PAMI-194_Mouse_U-Dd_TMT_40ug_28pctACN_25cm_120min_20160426_OT.raw"\t"F3.6"\t"2382.454129044"\t"2429.06773813294"\t"2707.24266676886"\t"3317.64996270132"\t"5035.09267261153"\t"3031.79934238544"\t"4808.55215766904"\t"2583.11478042214"\t"3103.61278056956"\t"2795.28295470917"\t""\t"40"\t"25.000"\t"18.000"\t"0.000380248968265973"\t"0.0008956"\t"0.01119"\r\n+"False"\t"High"\t"Mascot (C2)"\t"Unambiguous"\t"[K].aLEENNNFSk.[M]"\t"N-Term(TMT6plex); K10(TMT6plex)"\t"1"\t"1"\t""\t""\t"P55821"\t"Stathmin-2 OS=Mus musculus GN=Stmn2 PE=1 SV=1"\t"0"\t"2"\t""\t"0.0000"\t"1"\t"2"\t"812.44098"\t"1623.87468"\t"1623.87426"\t"0.26"\t"0.00021"\t"CID"\t"MS2"\t"20.48933"\t"0.8"\t"116.000"\t"38.9028"\t"7622"\t"PAMI-176_Mouse_A-J_TMT_40ug_22pctACN_25cm_120min_20160223_OT.raw"\t"F1.3"\t"1112.53015136719"\t""\t""\t""\t""\t"389.588287353516"\t"963.069763183594"\t""\t""\t""\t""\t"49"\t"29.000"\t"22.000"\t"9.32081629605059E-05"\t"0"\t"5.103E-05"\r\n+"False"\t"High"\t"Mascot (C2)"\t"Rejected"\t"[K].eMISDIk.[F]"\t"N-Term(TMT6plex); K7(TMT6plex)"\t"0"\t"1"\t""\t""\t"Q5SQM0"\t"Echinoderm microtubule-associated protein-like 6 OS=Mus musculus GN=Eml6 PE=2 SV=1"\t"0"\t"2"\t"0.0000"\t"0.0000"\t"1"\t"1"\t"647.37860"\t"1293.74993"\t"1293.74884"\t"0.84"\t"0.00054"\t"CID"\t"MS2"\t"62.11472"\t"25.4"\t"50.658"\t"45.5494"\t"10094"\t"PAMI-176_Mouse_A-J_TMT_40ug_24pctACN_25cm_120min_20160223_OT.raw"\t"F1.4"\t"8606.55904641178"\t"10042.301204891"\t"7976.23971232254"\t"5196.59941932638"\t"9381.06142410872"\t"12227.7069901572"\t"6418.27198828453"\t"5791.73957511049"\t"9665.49258896952"\t"5747.68029457234"\t""\t"11"\t"28.000"\t"21.000"\t"0.5635688125996"\t"0.001612"\t"0.02845"\r\n+"False"\t"High"\t"Mascot (C2)"\t"Unambiguous"\t"[KR].iIDFGLAR.[HQRT]"\t"N-Term(TMT6plex)"\t"4"\t"3"\t""\t""\t"Q3UIZ8; Q5SUV5; Q8VCR8"\t"Myosin light chain kinase 3 OS=Mus musculus GN=Mylk3 PE=1 SV=1; Myosin light chain kinase family member 4 OS=Mus musculus GN=Mylk4 PE=1 SV=2; Myosin light chain kinase 2, skeletal/cardiac muscle OS=Mus musculus GN=Mylk2 PE=1 SV=2"\t"0"\t"2"\t"0.0000"\t"0.0000"\t"1"\t"1"\t"567.34760"\t"1133.68791"\t"1133.68801"\t"-0.09"\t"-0.00005"\t"CID"\t"MS2"\t"30.28861"\t"13.5"\t"41.830"\t"70.4334"\t"19108"\t"PAMI-176_Mouse_A-J_TMT_40ug_30pctACN_25cm_120min_20160223_OT.raw"\t"F1.7"\t"4964.42868673888"\t"5950.64283137687"\t"3133.54920636473"\t"3321.0422704818"\t"2914.39733232664"\t"3274.3197320111"\t"3284.33337357729"\t"4714.29953279038"\t"3846.10503312523"\t"5461.43816436036"\t""\t"41"\t"24.000"\t"17.000"\t"0.000266256267358374"\t"9.826E-05"\t"0.0004159"\r\n+"False"\t"High"\t"Mascot (B2)"\t"Unambiguous"\t"[KR].iQLWDTAGQER.[FY]"\t"N-Term(TMT6plex)"\t"7"\t"1"\t""\t""\t"O35963"\t"Ras-related protein Rab-33B OS=Mus musculus GN=Rab33b PE=1 SV=1"\t"0"\t"3"\t""\t"0.0000"\t"1"\t"2"\t"515.94586"\t"1545.82303"\t"1545.82227"\t"0.49"\t"0.00025"\t"CID"\t"MS2"\t"14.17443"\t"5.2"\t"116.000"\t"63.1792"\t"15687"\t"PAMI-176_Mouse_K-T_TMT_40ug_26pctACN_25cm_120min_20160223_OT.raw"\t"F2.5"\t"2202.81245471708"\t"1313.99523020135"\t"'..b'"835.850341796875"\t""\t""\t""\t""\t""\t""\t""\t""\t""\t"53"\t"24.000"\t"17.000"\t"1.17095493273401E-05"\t"0"\t"6.158E-08"\r\n+"False"\t"High"\t"Mascot (B2)"\t"Unambiguous"\t"[R].iAQPNYIPTQQDVLR.[T]"\t"N-Term(TMT6plex)"\t"1"\t"1"\t"B2RSH2"\t"Guanine nucleotide-binding protein G(i) subunit alpha-1 OS=Mus musculus GN=Gnai1 PE=1 SV=1"\t"B2RSH2"\t"Guanine nucleotide-binding protein G(i) subunit alpha-1 OS=Mus musculus GN=Gnai1 PE=1 SV=1"\t"0"\t"3"\t"0.8846"\t"0.0000"\t"1"\t"1"\t"662.37213"\t"1985.10184"\t"1985.10174"\t"0.05"\t"0.00003"\t"CID"\t"MS2"\t"23.18596"\t"109.8"\t"40.825"\t"64.9133"\t"16311"\t"PAMI-176_Mouse_K-T_TMT_40ug_24pctACN_25cm_120min_20160223_OT.raw"\t"F2.4"\t"45678.6277106666"\t"40960.4336261915"\t"22655.0490232642"\t"46944.2568564104"\t"40149.5065460099"\t"33835.5156703187"\t"36006.7208517054"\t"33835.6633633171"\t"14265.9408252046"\t"32881.647549812"\t""\t"26"\t"28.000"\t"21.000"\t"0.016685241479773"\t"2.59E-05"\t"0.0001071"\r\n+"False"\t"High"\t"Mascot (B2)"\t"Unambiguous"\t"[K].lGGNYGPTVAVQR.[E]"\t"N-Term(TMT6plex)"\t"1"\t"1"\t"O35855"\t"Branched-chain-amino-acid aminotransferase, mitochondrial OS=Mus musculus GN=Bcat2 PE=1 SV=2"\t"O35855"\t"Branched-chain-amino-acid aminotransferase, mitochondrial OS=Mus musculus GN=Bcat2 PE=1 SV=2"\t"0"\t"3"\t"0.8163"\t"0.0000"\t"1"\t"1"\t"520.96136"\t"1560.86954"\t"1560.86956"\t"-0.01"\t"-0.00001"\t"CID"\t"MS2"\t"13.06845"\t"98.6"\t"26.884"\t"50.6059"\t"11062"\t"PAMI-176_Mouse_K-T_TMT_40ug_26pctACN_25cm_120min_20160223_OT.raw"\t"F2.5"\t"44503.0267413458"\t"37711.4239616076"\t"20172.0019617847"\t"35234.7128859956"\t"16349.9489921543"\t"17884.4898616459"\t"30106.8256702614"\t"53177.2692002148"\t"16039.6337456286"\t"34755.4383246068"\t""\t"49"\t"28.000"\t"21.000"\t"9.16420092852833E-05"\t"0"\t"1.181E-05"\r\n+"False"\t"High"\t"Mascot (C2)"\t"Unambiguous"\t"[R].lFRPWLNMDR.[M]"\t"N-Term(TMT6plex)"\t"1"\t"1"\t"O35855"\t"Branched-chain-amino-acid aminotransferase, mitochondrial OS=Mus musculus GN=Bcat2 PE=1 SV=2"\t"O35855"\t"Branched-chain-amino-acid aminotransferase, mitochondrial OS=Mus musculus GN=Bcat2 PE=1 SV=2"\t"1"\t"3"\t"0.6667"\t"0.0000"\t"1"\t"1"\t"526.29614"\t"1576.87387"\t"1576.86197"\t"7.55"\t"0.00397"\t"CID"\t"MS2"\t"24.11136"\t"17.3"\t"43.075"\t"101.3551"\t"21805"\t"PAMI-176_Mouse_A-J_TMT_40ug_90pctACN_25cm_120min_20160223_OT.raw"\t"F1.9"\t"2377.56565209098"\t"7463.3206110912"\t"5705.72881355803"\t"7036.69095329994"\t"4406.29948205538"\t"6147.36256595148"\t"5064.3216654225"\t"3941.1148326627"\t"3690.30046755331"\t"6644.04135510953"\t""\t"15"\t"29.000"\t"22.000"\t"0.262232475938664"\t"0.009059"\t"0.2173"\r\n+"False"\t"High"\t"Mascot (C2)"\t"Unambiguous"\t"[K].lGGNYGPTVAVQR.[E]"\t"N-Term(TMT6plex)"\t"1"\t"1"\t"O35855"\t"Branched-chain-amino-acid aminotransferase, mitochondrial OS=Mus musculus GN=Bcat2 PE=1 SV=2"\t"O35855"\t"Branched-chain-amino-acid aminotransferase, mitochondrial OS=Mus musculus GN=Bcat2 PE=1 SV=2"\t"0"\t"2"\t"0.8986"\t"0.0000"\t"1"\t"1"\t"780.93848"\t"1560.86968"\t"1560.86956"\t"0.08"\t"0.00006"\t"CID"\t"MS2"\t"13.13907"\t"18.8"\t"42.865"\t"44.7536"\t"9784"\t"PAMI-176_Mouse_A-J_TMT_40ug_24pctACN_25cm_120min_20160223_OT.raw"\t"F1.4"\t"5406.92044447944"\t"5700.45067176442"\t"5779.77396787467"\t"8121.57815927092"\t"5842.91904123047"\t"8366.40032091942"\t"4887.80678850218"\t"4493.25006067015"\t"5835.57342520261"\t"8483.5042549358"\t""\t"69"\t"28.000"\t"21.000"\t"9.57402600303558E-07"\t"0"\t"2.111E-06"\r\n+"False"\t"High"\t"Mascot (C2)"\t"Unambiguous"\t"[R].lFRPWLNMDR.[M]"\t"N-Term(TMT6plex)"\t"1"\t"1"\t"O35855"\t"Branched-chain-amino-acid aminotransferase, mitochondrial OS=Mus musculus GN=Bcat2 PE=1 SV=2"\t"O35855"\t"Branched-chain-amino-acid aminotransferase, mitochondrial OS=Mus musculus GN=Bcat2 PE=1 SV=2"\t"1"\t"3"\t"0.6364"\t"0.0000"\t"1"\t"1"\t"526.29449"\t"1576.86893"\t"1576.86197"\t"4.42"\t"0.00232"\t"CID"\t"MS2"\t"37.84634"\t"15.1"\t"39.910"\t"100.8119"\t"21603"\t"PAMI-176_Mouse_A-J_TMT_40ug_90pctACN_25cm_120min_20160223_OT.raw"\t"F1.9"\t"2555.12460251798"\t"6838.95023038471"\t"5760.48716888944"\t"5135.11469462554"\t"3511.43162272395"\t"5267.43689864942"\t"4277.03016267"\t"3501.84844459488"\t"3544.78542638775"\t"5409.12638344978"\t""\t"11"\t"28.000"\t"21.000"\t"0.583655083860827"\t"0.002008"\t"0.03542"\r\n'