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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins commit aaf1e94b225eb1b75837a9e65bf8c480d808287f"
author galaxyp
date Thu, 16 Sep 2021 19:31:46 +0000
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ecf5a558dc8a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins commit aaf1e94b225eb1b75837a9e65bf8c480d808287f"
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1 <tool id="proteomiqon_joinquantpepionswithproteins" name="Proteomiqon JoinQuantPepIonsWithProteins" version="@VERSION@" profile="20.05">
ecf5a558dc8a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins commit aaf1e94b225eb1b75837a9e65bf8c480d808287f"
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2 <description>
ecf5a558dc8a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins commit aaf1e94b225eb1b75837a9e65bf8c480d808287f"
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3 combines the results from ProteinInference and PSMBasedQuantification.
ecf5a558dc8a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins commit aaf1e94b225eb1b75837a9e65bf8c480d808287f"
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4 </description>
ecf5a558dc8a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins commit aaf1e94b225eb1b75837a9e65bf8c480d808287f"
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5 <macros>
ecf5a558dc8a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins commit aaf1e94b225eb1b75837a9e65bf8c480d808287f"
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6 <token name="@VERSION@">0.0.1</token>
ecf5a558dc8a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins commit aaf1e94b225eb1b75837a9e65bf8c480d808287f"
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7 </macros>
ecf5a558dc8a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins commit aaf1e94b225eb1b75837a9e65bf8c480d808287f"
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8 <requirements>
ecf5a558dc8a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins commit aaf1e94b225eb1b75837a9e65bf8c480d808287f"
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9 <requirement type="package" version="@VERSION@">proteomiqon-joinquantpepionswithproteins</requirement>
ecf5a558dc8a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins commit aaf1e94b225eb1b75837a9e65bf8c480d808287f"
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10 </requirements>
ecf5a558dc8a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins commit aaf1e94b225eb1b75837a9e65bf8c480d808287f"
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11 <command detect_errors="exit_code"><![CDATA[
ecf5a558dc8a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins commit aaf1e94b225eb1b75837a9e65bf8c480d808287f"
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12 #import re
ecf5a558dc8a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins commit aaf1e94b225eb1b75837a9e65bf8c480d808287f"
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13 #set quant_basename = $re.sub(r'[^\w ,.\-+]','_',$quantifiedpeptides.element_identifier)
ecf5a558dc8a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins commit aaf1e94b225eb1b75837a9e65bf8c480d808287f"
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14 ln -s '$quantifiedpeptides' '${quant_basename}.quant' &&
ecf5a558dc8a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins commit aaf1e94b225eb1b75837a9e65bf8c480d808287f"
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15 #set prot_basename = $re.sub(r'[^\w ,.\-+]','_',$inferredproteins.element_identifier)
ecf5a558dc8a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins commit aaf1e94b225eb1b75837a9e65bf8c480d808287f"
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16 ln -s '$inferredproteins' '${prot_basename}.prot' &&
ecf5a558dc8a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins commit aaf1e94b225eb1b75837a9e65bf8c480d808287f"
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17 ln -s '$out_quantAndProt' '${quant_basename}.quantAndProt' &&
ecf5a558dc8a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins commit aaf1e94b225eb1b75837a9e65bf8c480d808287f"
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18 proteomiqon-joinquantpepionswithproteins -i '${quant_basename}.quant' -ii '${prot_basename}.prot' -o './'
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19 ]]>
ecf5a558dc8a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins commit aaf1e94b225eb1b75837a9e65bf8c480d808287f"
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20 </command>
ecf5a558dc8a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins commit aaf1e94b225eb1b75837a9e65bf8c480d808287f"
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21 <inputs>
ecf5a558dc8a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins commit aaf1e94b225eb1b75837a9e65bf8c480d808287f"
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22 <param name="quantifiedpeptides" type="data" format="tabular" label="Quantified Peptides" help="Specify Quantified Peptides." />
ecf5a558dc8a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins commit aaf1e94b225eb1b75837a9e65bf8c480d808287f"
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23 <param name="inferredproteins" type="data" format="tabular" label="Inferred Proteins" help="Specify Inferred Proteins." />
ecf5a558dc8a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins commit aaf1e94b225eb1b75837a9e65bf8c480d808287f"
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24 </inputs>
ecf5a558dc8a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins commit aaf1e94b225eb1b75837a9e65bf8c480d808287f"
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25 <outputs>
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26 <data format="tabular" name="out_quantAndProt" />
ecf5a558dc8a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins commit aaf1e94b225eb1b75837a9e65bf8c480d808287f"
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27 </outputs>
ecf5a558dc8a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins commit aaf1e94b225eb1b75837a9e65bf8c480d808287f"
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28 <tests>
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29 <test expect_num_outputs="1">
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30 <param name="quantifiedpeptides" value="sample.quant"/>
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31 <param name="inferredproteins" value="sample.prot"/>
ecf5a558dc8a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins commit aaf1e94b225eb1b75837a9e65bf8c480d808287f"
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32 <output name="out_quantAndProt" file="sample_out.quantAndProt"/>
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33 </test>
ecf5a558dc8a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins commit aaf1e94b225eb1b75837a9e65bf8c480d808287f"
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34 </tests>
ecf5a558dc8a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins commit aaf1e94b225eb1b75837a9e65bf8c480d808287f"
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35 <help>
ecf5a558dc8a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins commit aaf1e94b225eb1b75837a9e65bf8c480d808287f"
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36 <![CDATA[
ecf5a558dc8a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins commit aaf1e94b225eb1b75837a9e65bf8c480d808287f"
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37 What It Does
ecf5a558dc8a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins commit aaf1e94b225eb1b75837a9e65bf8c480d808287f"
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38 ------------
ecf5a558dc8a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins commit aaf1e94b225eb1b75837a9e65bf8c480d808287f"
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39 **Disclaimer** this tool needs the results from ProteinInference and PSMBasedQuantification.
ecf5a558dc8a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins commit aaf1e94b225eb1b75837a9e65bf8c480d808287f"
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40
ecf5a558dc8a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins commit aaf1e94b225eb1b75837a9e65bf8c480d808287f"
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41 Results from PSMBasedQuantification contain detailed information about the quantification of every peptide, but only basic informations about the protein they
ecf5a558dc8a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins commit aaf1e94b225eb1b75837a9e65bf8c480d808287f"
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42 originated from. This information is obtained during the ProteinInference. This tool takes the results from both tools and combines the qauntification information of
ecf5a558dc8a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins commit aaf1e94b225eb1b75837a9e65bf8c480d808287f"
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43 each peptide with the more accurate information about the corresponding protein including its q-value.
ecf5a558dc8a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins commit aaf1e94b225eb1b75837a9e65bf8c480d808287f"
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44
ecf5a558dc8a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins commit aaf1e94b225eb1b75837a9e65bf8c480d808287f"
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45 Further Reading
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46 ---------------
ecf5a558dc8a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins commit aaf1e94b225eb1b75837a9e65bf8c480d808287f"
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47 Additional information about the tool can be found in the `documentation <https://csbiology.github.io/ProteomIQon/tools/JoinQuantPepIonsWithProteins.html>`_.
ecf5a558dc8a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins commit aaf1e94b225eb1b75837a9e65bf8c480d808287f"
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48 ]]>
ecf5a558dc8a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins commit aaf1e94b225eb1b75837a9e65bf8c480d808287f"
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49 </help>
ecf5a558dc8a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins commit aaf1e94b225eb1b75837a9e65bf8c480d808287f"
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50 </tool>