diff proteomiqon_joinquantpepionswithproteins.xml @ 0:ecf5a558dc8a draft default tip

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins commit aaf1e94b225eb1b75837a9e65bf8c480d808287f"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/proteomiqon_joinquantpepionswithproteins.xml	Thu Sep 16 19:31:46 2021 +0000
@@ -0,0 +1,50 @@
+<tool id="proteomiqon_joinquantpepionswithproteins" name="Proteomiqon JoinQuantPepIonsWithProteins" version="@VERSION@" profile="20.05">
+    <description>
+        combines the results from ProteinInference and PSMBasedQuantification.
+    </description>
+    <macros>
+        <token name="@VERSION@">0.0.1</token>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@VERSION@">proteomiqon-joinquantpepionswithproteins</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        #import re
+        #set quant_basename = $re.sub(r'[^\w ,.\-+]','_',$quantifiedpeptides.element_identifier)
+        ln -s '$quantifiedpeptides' '${quant_basename}.quant' &&
+        #set prot_basename = $re.sub(r'[^\w ,.\-+]','_',$inferredproteins.element_identifier)
+        ln -s '$inferredproteins' '${prot_basename}.prot' &&
+        ln -s '$out_quantAndProt' '${quant_basename}.quantAndProt' &&  
+        proteomiqon-joinquantpepionswithproteins -i '${quant_basename}.quant' -ii '${prot_basename}.prot' -o './'
+    ]]>
+    </command>
+    <inputs>
+        <param name="quantifiedpeptides" type="data" format="tabular" label="Quantified Peptides" help="Specify Quantified Peptides." />
+        <param name="inferredproteins" type="data" format="tabular" label="Inferred Proteins" help="Specify Inferred Proteins." />
+    </inputs>
+    <outputs>
+        <data format="tabular" name="out_quantAndProt" />
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="quantifiedpeptides" value="sample.quant"/>
+            <param name="inferredproteins" value="sample.prot"/>
+            <output name="out_quantAndProt" file="sample_out.quantAndProt"/>
+        </test>
+    </tests>
+    <help>
+    <![CDATA[
+What It Does
+------------
+**Disclaimer** this tool needs the results from ProteinInference and PSMBasedQuantification.
+
+Results from PSMBasedQuantification contain detailed information about the quantification of every peptide, but only basic informations about the protein they 
+originated from. This information is obtained during the ProteinInference. This tool takes the results from both tools and combines the qauntification information of
+each peptide with the more accurate information about the corresponding protein including its q-value.
+
+Further Reading
+---------------
+Additional information about the tool can be found in the `documentation <https://csbiology.github.io/ProteomIQon/tools/JoinQuantPepIonsWithProteins.html>`_.  
+    ]]>
+    </help>
+</tool>
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