diff FastaStats.xml @ 0:163892325845 draft default tip

Initial commit.

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+++ b/FastaStats.xml	Fri May 10 17:15:08 2013 -0400
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+<!-- 
+# =====================================================
+# $Id: FastaStats.xml 90 2011-01-19 13:20:31Z [e-mail] $
+# $URL: https://trac.nbic.nl/svn/galaxytools/trunk/tools/general/FastaTools/FastaStats.xml $
+# $LastChangedDate: 2011-01-19 07:20:31 -0600 (Wed, 19 Jan 2011) $ 
+# $LastChangedRevision: 90 $
+# $LastChangedBy: [e-mail] $
+# =====================================================
+-->
+<tool id="FastaStats1" name="FastaStats">
+  <description>List statistics for sequences in a FASTA file</description>
+  <command interpreter="perl">FastaStats.pl $get_positional_composition_stats -i $input -o $output -l WARN</command>
+  <inputs>
+    <param format="fasta" name="input" type="data" label="FASTA sequences"/>
+    <param name="get_positional_composition_stats" type="boolean" truevalue="-p" falsevalue="" optional="true" label="Calculate positional acid frequencies"/>
+  </inputs>
+  <outputs>
+    <data format="txt" name="output" label="FASTA Statistics for ${input.name}"/>
+  </outputs>
+  <tests>
+    <test>
+      <param name="input"       value="fasta_2_proteins.fasta" ftype="fasta"/>
+      <output name="output"     file="FastaStats_example_output.txt"/>
+    </test>
+  </tests>
+  <help>
+
+.. class:: infomark
+
+**What it does**
+
+This tool analyzes a collection of sequences in FASTA format and reports: \
+
+ - The total number of sequences.
+ - The total number of nucleotide or amino acids.
+ - The total frequency of nucleotide or amino acids.
+ - The positional frequency of nucleotide or amino acids (optional).
+ 
+-----
+
+**Example**
+
+If the FASTA sequence collection contains these two sequences::
+
+	&gt;UniProtKB:Q42593 L-ascorbate peroxidase T, chloroplastic;
+	MSVSLSAASHLLCSSTRVSLSPAVTSSSSSPVVALSSSTSPHSLGSVASSSLFPHSSFVL
+	QKKHPINGTSTRMISPKCAASDAAQLISAKEDIKVLLRTKFCHPILVRLGWHDAGTYNKN
+	IEEWPLRGGANGSLRFEAELKHAANAGLLNALKLIQPLKDKYPNISYADLFQLASATAIE
+	EAGGPDIPMKYGRVDVVAPEQCPEEGRLPDAGPPSPADHLRDVFYRMGLDDKEIVALSGA
+	HTLGRARPDRSGWGKPETKYTKTGPGEAGGQSWTVKWLKFDNSYFKDIKEKRDDDLLVLP
+	TDAALFEDPSFKNYAEKYAEDVAAFFKDYAEAHAKLSNLGAKFDPPEGIVIENVPEKFVA
+	AKYSTGKKELSDSMKKKIRAEYEAIGGSPDKPLPTNYFLNIIIAIGVLVLLSTLFGGNNN
+	SDFSGF
+	&gt;UniProtKB:A0MQ79 Ascorbate peroxidase;
+	MVKNYPVVSEEYLIAVDKAKKKLRGFIAEKNCAPLMLRLAWHSAGTFDQCSRTGGPFGTM
+	RFKAEQAHSANNGIDIAIRLLEPIKEQFPILSYADFYQLAGVVAVEVTGGPEVPFHPGRP
+	DKEEPPVEGRLPDAYKGSDHLRDVFIKQMGLSDQDIVALSGGHTLGRCHKERSGFEGPWT
+	ENPLIFDNSYFKELVCGERDGLLQLPSDKALLADPVFHPLVEKYAADEDAFFADYAEAHL
+	KLSELGFADA
+
+The reported stats (without optional positional acid frequencies) will be this::
+   
+	Sequences	2
+	Acid A		69
+	Acid C		8
+	Acid D		44
+	Acid E		44
+	Acid F		33
+	Acid G		52
+	Acid H		18
+	Acid I		30
+	Acid K		50
+	Acid L		67
+	Acid M		9
+	Acid N		22
+	Acid P		46
+	Acid Q		13
+	Acid R		26
+	Acid S		57
+	Acid T		23
+	Acid V		37
+	Acid W		7
+	Acid Y		21
+	Total acids	676
+
+  </help>
+</tool>