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/tools/emboss_5/emboss_dan.xml

https://bitbucket.org/cistrome/cistrome-harvard/
XML | 90 lines | 66 code | 4 blank | 20 comment | 0 complexity | 5aa0ef0dcac230aeca3b5a59919fda33 MD5 | raw file
 1<tool id="EMBOSS: dan19" name="dan" version="5.0.0">
 2  <description>Calculates DNA RNA/DNA melting temperature</description>
 3  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
 4  <command interpreter="perl">emboss_single_outputfile_wrapper.pl dan -sequence $input1 -windowsize $window -goutfile $out_file1 -graph png -plot $plot1 -shiftincrement $shift -dnaconc $dnaconc
 5  -saltconc $saltconc -product $product -formamide $formamide -mismatch $mismatch -prodlen $prodlen -thermo $thermo -temperature $temperature -rna $rna -outfile $out_file1 -auto</command>
 6  <inputs>
 7    <param format="data" name="input1" type="data">
 8      <label>On query</label>
 9    </param>
10    <param name="window" size="4" type="text" value="20">
11      <label>Window Size</label>
12    </param>
13    <param name="shift" size="4" type="text" value="1">
14      <label>Step size (shift increment)</label>
15    </param>
16    <param name="dnaconc" size="4" type="text" value="50.0">
17      <label>DNA Concentration (nM)</label>
18    </param>
19    <param name="saltconc" size="4" type="text" value="50.0">
20      <label>Salt concentration (mM)</label>
21    </param>
22    <param name="thermo" type="select">
23      <label>Output the DeltaG, DeltaH and DeltaS values</label>
24      <option value="yes">Yes</option>
25      <option value="no">No</option>
26    </param>
27    <param name="temperature" size="4" type="text" value="25 ">
28      <label>Temperature at which to calculate the DeltaG, DeltaH and DeltaS values</label>
29    </param>
30    <param name="rna" type="select">
31      <label>Sequence is RNA</label>
32      <option value="no">No</option>
33      <option value="yes">Yes</option>
34    </param>
35    <param name="product" type="select">
36      <label>Include percent formamide, percent of mismatches allowed and product length</label>
37      <option value="no">No</option>
38      <option value="yes">Yes</option>
39    </param>
40    <param name="formamide" size="4" type="text" value="0 ">
41      <label>Formamide concentration (nM)</label>
42    </param>
43    <param name="mismatch" size="4" type="text" value="0 ">
44      <label>Percent mismatch to be used in calculations</label>
45    </param>
46    <param name="prodlen" size="4" type="text" value="20">
47      <label>Product length to be used in calculations</label>
48    </param>
49    <param name="plot1" type="select">
50      <label>Create a graph</label>
51      <option value="no">No</option>
52      <option value="yes">Yes</option>
53    </param>
54  </inputs>
55  <outputs>
56    <data format="dan" name="out_file1" />
57  </outputs>
58  <!--
59  <tests>
60    <test>
61      <param name="input1" value="2.fasta"/>
62      <param name="window" value="20"/>
63      <param name="shift" value="1"/>
64      <param name="dnaconc" value="50"/>
65      <param name="saltconc" value="50"/>
66      <param name="thermo" value="yes"/>
67      <param name="temperature" value="25"/>
68      <param name="rna" value="no"/>
69      <param name="product" value="no"/>
70      <param name="formamide" value="0"/>
71      <param name="mismatch" value="0"/>
72      <param name="prodlen" value="20"/>
73      <param name="plot1" value="yes"/>
74      <output name="out_file1" file="emboss_dan_out.png"/>
75    </test>
76  </tests>
77  -->
78  <code file="emboss_format_corrector.py" />
79  <help>
80    You can view the original documentation here_.
81    
82    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/dan.html
83
84------
85
86**Citation**
87
88If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
89  </help>
90</tool>