diff dnp_select_range.xml @ 0:c0c35d9cd215 draft default tip

"planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/dnp_select_range.xml	Fri May 01 12:07:01 2020 +0000
@@ -0,0 +1,69 @@
+<tool id="dnp_select_range" name="Select interval" version="0.1.0">
+    <requirements>
+    </requirements>
+    <command detect_errors="exit_code" interpreter="sh"><![CDATA[
+        dnp-select-range.sh "$input1" "$input2" "$input3" "$input4" "$output1" 
+    ]]></command>
+    <inputs>
+
+       <param type="data" name="input1" format="tabular" label="Table of profiles"/>
+        <param name="input2" type="integer" value="20"    label="Start position" />
+        <param name="input3" type="integer" value="146"  label="Size of selection" />
+        <param name="input4" type="text"    value="AA AC AG AT CA CC CG CT GA GC GG GT TA TC TG TT" label="Dinucleotides" />
+    </inputs>
+    <outputs>
+        <data name="output1" format="tabular" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input1" value="select-range-input.tabular"/>
+            <param name="input2" value="20"/>
+            <param name="input3" value="146"/>
+            <param name="input4" value="AA AC AG AT CA CC CG CT GA GC GG GT TA TC TG TT"/>
+            <output name="output1" file="select-range-output.tabular"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+        
+Description::
+
+   Selects rows from input table within a given range and adds a column with positional information.
+   An example below shows a selection starting from row=20.
+
+Example::
+
+   Input tabular:
+
+   AA.f	        AA.r	        AC.f	        AC.r	        AG.f	        AG.r	        AT.f	        AT.r       ...
+   0.0763         0.067920	0.057800	0.078120	0.081600	0.061960	0.055600	0.044080
+   0.077160	0.073760	0.056000	0.072160	0.079400	0.060720	0.055960	0.047040
+   0.083320	0.071200	0.053840	0.080760	0.084560	0.064880	0.050440	0.048720
+   0.077960	0.068200	0.056040	0.075520	0.080120	0.061680	0.053160	0.047400
+   0.078200	0.069120	0.056880	0.074000	0.084360	0.060840	0.053520	0.046280
+   ... 
+
+   Output tabular:
+
+   pos	AA.f	        AC.f	        AG.f	        AT.f	        CA.f	        CC.f	        CG.f	        CT.f     ...
+   20	0.100200	0.084720	0.077200	0.072480	0.066160	0.044160	0.004560	0.060720
+   21	0.172440	0.024800	0.002080	0.101240	0.131840	0.007200	0.000320	0.095920
+   22	0.077160	0.096240	0.314320	0.047360	0.012040	0.028560	0.011840	0.013680
+   ...
+
+
+    ]]></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>