diff dnp_binary_strings.xml @ 0:611156829647 draft default tip

"planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/dnp_binary_strings.xml	Fri May 01 12:07:46 2020 +0000
@@ -0,0 +1,61 @@
+<tool id="dnp_binary_strings" name="Binary strings from fasta" version="0.1.0">
+    <requirements>
+        <requirement type="package" version="1.0">dnp-binstrings</requirement>
+    </requirements>
+    <command detect_errors="exit_code" interpreter="sh"><![CDATA[
+        dnp-binary-strings.sh '$input1' '$input2' '$output1'
+    ]]></command>
+    <inputs>
+      <param type="data" name="input1" format="fasta" label="From fasta" />
+      <param name="input2" type="text" value="AA AC" label="Dinucleotides" />
+    </inputs>
+    <outputs>
+        <data name="output1" format="tabular" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input1" value="seq4.fasta"/>
+            <param name="input2" value="AA AC"/>
+            <output name="output1" file="seq4.tabular"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+Description::
+
+
+   Convert fasta sequences to a binary sequence of 01 
+   in which ones indicate a presence of a given 
+   dinucleotide at that position.
+
+   Each input fasta sequence has a corresponding output
+   row with tab separated columns- binary string, dinucleotide,  
+   original fasta string, number of the dinucleotide occurrences
+
+
+Example::
+
+   Input fasta:
+      chr9:42475963-42476182 
+      CCAGGCAGACCCCATA
+   
+   Output tabular:
+      100000000111000 CC chr9:42475963-42476182 CCAGGCAGACCCCATA 4
+
+
+    ]]></help>
+    <citations>
+        <citation type="bibtex">
+@article{pranckeviciene2020nucleosome,
+  title={Nucleosome positioning sequence patterns as packing or regulatory. S1 Appendix},
+  author={Pranckeviciene, Erinija and Hosid, Sergey and Liang, Nathan and Ioshikhes, Ilya},
+  journal={PLoS computational biology},
+  volume={16},
+  number={1},
+  pages={e1007365},
+  year={2020},
+  publisher={Public Library of Science},
+  url = {https://doi.org/10.1371/journal.pcbi.1007365}
+}</citation>
+    </citations>
+</tool>