diff PDAUG_Peptide_Ngrams/PDAUG_Peptide_Ngrams.xml @ 0:7557b48b2872 draft

"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/PDAUG_Peptide_Ngrams/PDAUG_Peptide_Ngrams.xml	Wed Oct 28 02:10:12 2020 +0000
@@ -0,0 +1,76 @@
+<tool id="pdaug_peptide_ngrams" name="PDAUG Peptide Ngrams" version="0.1.0" python_template_version="2.7">
+	<description>Counts n-grams in the entire sequence set and fitting their distribution with the power-law distribution (Zipf’s law)</description>
+  
+    <requirements>
+      <requirement type="package" version="2.7.18">python</requirement>
+      <requirement type="package" version="1.4.6">powerlaw</requirement>
+      <requirement type="package" version="0.2.4">quantiprot</requirement>
+    </requirements>
+
+    <command detect_errors="exit_code"><![CDATA[
+
+        python2 '$__tool_directory__/PDAUG_Peptide_Ngrams.py' -f1 '$fasta1' -f2 '$fasta2'  --OutFile 'out.png'
+             
+    ]]></command>
+
+    <inputs>
+      <param name="fasta1" type="data" format="fasta" label="First fasta file" argument= "--fasta1" help="First fasta file"/>
+      <param name="fasta2" type="data" format="fasta" label="Second fasta file" argument= "--fasta2" help="First fasta file"/>
+    </inputs>
+
+    <outputs>   
+        <data name='output2' format='png' label="${tool.name} on $on_string - (PNG)" from_work_dir="out.png"/>
+    </outputs>
+ 
+    <tests>
+        <test>
+            <param name="fasta1" value="test1.fasta"/>
+            <param name="fasta2" value="test2.fasta"/>
+            <output name="output2" file="out.png"/>
+        </test>
+    </tests>
+
+    <help><![CDATA[
+.. class:: infomark
+
+**What it does**
+
+This tool counts n-grams in the entire  peptide sequence set and fitting their distribution with the power-law distribution (Zipf’s law) and plot the results.
+
+-----
+
+**Inputs**
+    * **--InFile** Takes fasta file as input with peptide sequences. 
+
+-----
+
+**Outputs**
+    * Returns html report file.]]></help>
+<citations>
+  <citation type="bibtex">
+    @misc{PDAUGGITHUB, 
+      author = {Joshi, Jayadev  and Blankenberg, Daniel}, 
+      year = {2020}, 
+      title ={PDAUG - a Galaxy based toolset for peptide library analysis, visualization, and machine learning modeling}, 
+      publisher = {GitHub}, 
+      journal = {GitHub repository}, 
+      url =
+      {https://github.com/jaidevjoshi83/pdaug.git}, 
+      }
+  </citation>
+  <citation type="bibtex">
+    @article{konopka_marciniak_dyrka_2017,
+       title={Quantiprot - a Python package for quantitative analysis of protein sequences}, 
+       volume={18},
+       DOI={10.1186/s12859-017-1751-4}, 
+       number={1}, 
+       journal={BMC Bioinformatics},
+       author={Konopka, Bogumił M. and Marciniak, Marta and Dyrka, Witold}, 
+       year={2017}
+     }
+  </citation>
+</citations>
+</tool>
+
+
+