From f077afa4366d788daf9750fc0abeba8cc112278d Mon Sep 17 00:00:00 2001
From: Wen-Yu Chung <wychung@bx.psu.edu>
Date: Tue, 5 Feb 2008 18:32:42 +0000
Subject: [PATCH] update several xml files for better help descriptions. modify
 section names and ids in tool_conf.xml.sample: Fasta Tools -> FASTA
 manipulation Metagenomics -> Short Read Analysis remove
 short_reads_figure_length from tool_conf.xml.sample.

---
 tool_conf.xml.sample                          |  5 +-
 tools/fasta_tools/fasta_to_tabular.xml        | 15 ++---
 .../fasta_tools/fasta_tool_compute_length.xml | 35 ++++--------
 .../fasta_tool_filter_by_length.xml           | 53 +++++------------
 tools/fasta_tools/tabular_to_fasta.xml        | 12 ----
 .../metag_tools/short_reads_figure_score.xml  | 18 ++----
 tools/metag_tools/short_reads_trim_seq.xml    | 57 ++++---------------
 7 files changed, 48 insertions(+), 147 deletions(-)

diff --git a/tool_conf.xml.sample b/tool_conf.xml.sample
index 5bfcb01a35c..e676620993e 100644
--- a/tool_conf.xml.sample
+++ b/tool_conf.xml.sample
@@ -311,13 +311,12 @@
     <tool file="emboss_5/emboss_wordmatch.xml" /> 
   </section> 
   -->
-  <section name="Fasta Tools" id="fasta_tools">
+  <section name="FASTA manipulation" id="fasta_manipulation">
     <tool file="fasta_tools/fasta_tool_compute_length.xml" />
     <tool file="fasta_tools/fasta_tool_filter_by_length.xml" />
   </section>
-  <section name="Metagenomics" id="metagenomics">
+  <section name="Short Read Analysis" id="short_read_analysis">
     <tool file="metag_tools/short_reads_trim_seq.xml" />
     <tool file="metag_tools/short_reads_figure_score.xml" />
-    <tool file="metag_tools/short_reads_figure_length.xml" />
  </section>
 </toolbox>
diff --git a/tools/fasta_tools/fasta_to_tabular.xml b/tools/fasta_tools/fasta_to_tabular.xml
index 06754d17ebd..8f55936e8d3 100644
--- a/tools/fasta_tools/fasta_to_tabular.xml
+++ b/tools/fasta_tools/fasta_to_tabular.xml
@@ -23,18 +23,15 @@
 
 A fasta file with two sequences::
 
-	&gt;EYKX4VC01B65GS length=54 xy=0784_1754 region=1 run=R_2007_11_07_16_15_57_
-	CCGGTATCCGGGTGCCGTGATGAGCGCCACCGGAACGAATTCGACTATGCCGAA
-	&gt;EYKX4VC01BNCSP length=187 xy=0558_3831 region=1 run=R_2007_11_07_16_15_57_
-	CTTACCGGTCACCACCGTGCCTTCAGGATTGATCGCCAGATCGGTCGGTGCGTCAGGCGG
-	GGTGACATCGCCCACCACGGTACTCACTGGCTGGCTCTGGTTCCCGGCGGCATCGGAGGC
-	CACCACGTTGAGGGTATTCCCCTCGGTTTGTGGCTCGGTGAGAACCACGTTGTAGTCGCC
-	ATTGGTC
+	&gt;seq1
+	CCGGTATCCG
+	&gt;seq2
+	CTTACC
 
 Returns::
 
-	&gt;EYKX4VC01B65GS length=54 xy=0784_1754 region=1 run=R_2007_11_07_16_15_57_	CCGGTATCCGGGTGCCGTGATGAGCGCCACCGGAACGAATTCGACTATGCCGAA
-	&gt;EYKX4VC01BNCSP length=187 xy=0558_3831 region=1 run=R_2007_11_07_16_15_57_	CTTACCGGTCACCACCGTGCCTTCAGGATTGATCGCCAGATCGGTCGGTGCGTCAGGCGGGGTGACATCGCCCACCACGGTACTCACTGGCTGGCTCTGGTTCCCGGCGGCATCGGAGGCCACCACGTTGAGGGTATTCCCCTCGGTTTGTGGCTCGGTGAGAACCACGTTGTAGTCGCCATTGGTC
+	&gt;seq1	CCGGTATCCG
+	&gt;seq2	CTTACC
 
 	</help>
 </tool>
\ No newline at end of file
diff --git a/tools/fasta_tools/fasta_tool_compute_length.xml b/tools/fasta_tools/fasta_tool_compute_length.xml
index 6858d97d78f..430ee6441b7 100644
--- a/tools/fasta_tools/fasta_tool_compute_length.xml
+++ b/tools/fasta_tools/fasta_tool_compute_length.xml
@@ -23,34 +23,19 @@
 
 Fasta Sequence::
 
-	&gt;hg17_chr1_147962192_147962580_+
-	TCATTTAATGACAATTTTCTGGCGCAAGGCTCGGGGCCCAGAGCCAGGGA
-	GGGGCTCAGGAGGTGGCGGGCCGGGGCCCAGGGCTGAGGCAGTGGGCGGC
-	AGTCCATGGGCAGTAATGTACTTCTTGTAAGCCTCACGAATGATCTTGAA
-	GGCTCGAGCAGTGGCATAGGGTATGTCTGTAACAGGGTCCCGGTATAGGG
-	CTGGACGATGGGTCACTGGACAGACCTCACGAACAGGGACTTTTGGGGGC
-	CGCCCTTGGGGGAACCATTCCTCGAAAGTTGCATCATCACTAAAAGTGAT
-	GAAGGTACGTGAGCAGCGAGCAGGGGGGTTGACGGGTCCAGTCCCAGCAT
-	GAGGAGTCAATGCAGACACCGAGGGAGCAGGATCAAGT
-	&gt;hg17_chr1_147984545_147984630_+
-	ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTT
-	TGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG
-	&gt;hg17_chr1_148078400_148078582_+
-	TCACATGATGCCGTTGGTGAGGTACTGGAAGCCGTCATAGAGTTTGGTGG
-	TGATAGACCGCATACTGCCATCCACCATCTGCTCCACCAGCAGCTGCAGC
-	TGCTCCTCAGTCATGCTCATGTGGAACCTCTCTTTGAGGTTTCGAATGGT
-	GCTGGAGCCATGGAAGCAAGGAAGCTGAGAAC
-	&gt;hg17_chr1_148185136_148185276_+
-	ATGGAAGCGTTTTTGGGGTCGCGGTCCGGACTTTGGGCGGGGGGTCCGGC
-	CCCAGGACAGTTTTACCGCATTCCGTCCACTCCCGATTCCTTCATGGATC
-	CGGCGTCTGCACTTTACAGAGGTCCAATCACGCGGACCCA
+	&gt;seq1
+	TCATTTA
+	&gt;seq2
+	ATGGCGTCGGCC
+	&gt;seq3
+	TCACATGATG
 
 Returns::
 	
-	&gt;hg17_chr1_147962192_147962580_+	388
-	&gt;hg17_chr1_147984545_147984630_+	85
-	&gt;hg17_chr1_148078400_148078582_+	182
-	&gt;hg17_chr1_148185136_148185276_+	140	
+	&gt;seq1	7
+	&gt;seq2	12
+	&gt;seq3	10
+	
 
 	</help>
 </tool>
\ No newline at end of file
diff --git a/tools/fasta_tools/fasta_tool_filter_by_length.xml b/tools/fasta_tools/fasta_tool_filter_by_length.xml
index 8092673990d..b7ad60c7c90 100644
--- a/tools/fasta_tools/fasta_tool_filter_by_length.xml
+++ b/tools/fasta_tools/fasta_tool_filter_by_length.xml
@@ -23,48 +23,21 @@
 
 Fasta Sequence::
 
-	&gt;hg17_chr1_147962192_147962580_+
-	TCATTTAATGACAATTTTCTGGCGCAAGGCTCGGGGCCCAGAGCCAGGGA
-	GGGGCTCAGGAGGTGGCGGGCCGGGGCCCAGGGCTGAGGCAGTGGGCGGC
-	AGTCCATGGGCAGTAATGTACTTCTTGTAAGCCTCACGAATGATCTTGAA
-	GGCTCGAGCAGTGGCATAGGGTATGTCTGTAACAGGGTCCCGGTATAGGG
-	CTGGACGATGGGTCACTGGACAGACCTCACGAACAGGGACTTTTGGGGGC
-	CGCCCTTGGGGGAACCATTCCTCGAAAGTTGCATCATCACTAAAAGTGAT
-	GAAGGTACGTGAGCAGCGAGCAGGGGGGTTGACGGGTCCAGTCCCAGCAT
-	GAGGAGTCAATGCAGACACCGAGGGAGCAGGATCAAGT
-	&gt;hg17_chr1_147984545_147984630_+
-	ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTT
-	TGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG
-	&gt;hg17_chr1_148078400_148078582_+
-	TCACATGATGCCGTTGGTGAGGTACTGGAAGCCGTCATAGAGTTTGGTGG
-	TGATAGACCGCATACTGCCATCCACCATCTGCTCCACCAGCAGCTGCAGC
-	TGCTCCTCAGTCATGCTCATGTGGAACCTCTCTTTGAGGTTTCGAATGGT
-	GCTGGAGCCATGGAAGCAAGGAAGCTGAGAAC
-	&gt;hg17_chr1_148185136_148185276_+
-	ATGGAAGCGTTTTTGGGGTCGCGGTCCGGACTTTGGGCGGGGGGTCCGGC
-	CCCAGGACAGTTTTACCGCATTCCGTCCACTCCCGATTCCTTCATGGATC
-	CGGCGTCTGCACTTTACAGAGGTCCAATCACGCGGACCCA
+	&gt;seq1
+	TCATTTAATGAC
+	&gt;seq2
+	ATGGC
+	&gt;seq3
+	TCACATGATGCCG
+	&gt;seq4
+	ATGGAAGC
 
-Choose minimal length as 100, maximal length as 0 (no limitation), the tool returns::
+Choose minimal length as 10, maximal length as 0 (no limitation), the tool returns::
 
-	&gt;hg17_chr1_147962192_147962580_+
-	TCATTTAATGACAATTTTCTGGCGCAAGGCTCGGGGCCCAGAGCCAGGGA
-	GGGGCTCAGGAGGTGGCGGGCCGGGGCCCAGGGCTGAGGCAGTGGGCGGC
-	AGTCCATGGGCAGTAATGTACTTCTTGTAAGCCTCACGAATGATCTTGAA
-	GGCTCGAGCAGTGGCATAGGGTATGTCTGTAACAGGGTCCCGGTATAGGG
-	CTGGACGATGGGTCACTGGACAGACCTCACGAACAGGGACTTTTGGGGGC
-	CGCCCTTGGGGGAACCATTCCTCGAAAGTTGCATCATCACTAAAAGTGAT
-	GAAGGTACGTGAGCAGCGAGCAGGGGGGTTGACGGGTCCAGTCCCAGCAT
-	GAGGAGTCAATGCAGACACCGAGGGAGCAGGATCAAGT
-	&gt;hg17_chr1_148078400_148078582_+
-	TCACATGATGCCGTTGGTGAGGTACTGGAAGCCGTCATAGAGTTTGGTGG
-	TGATAGACCGCATACTGCCATCCACCATCTGCTCCACCAGCAGCTGCAGC
-	TGCTCCTCAGTCATGCTCATGTGGAACCTCTCTTTGAGGTTTCGAATGGT
-	GCTGGAGCCATGGAAGCAAGGAAGCTGAGAAC
-	&gt;hg17_chr1_148185136_148185276_+
-	ATGGAAGCGTTTTTGGGGTCGCGGTCCGGACTTTGGGCGGGGGGTCCGGC
-	CCCAGGACAGTTTTACCGCATTCCGTCCACTCCCGATTCCTTCATGGATC
-	CGGCGTCTGCACTTTACAGAGGTCCAATCACGCGGACCCA
+	&gt;seq1
+	TCATTTAATGAC
+	&gt;seq3
+	TCACATGATGCCG
 
 	</help>
 </tool>
\ No newline at end of file
diff --git a/tools/fasta_tools/tabular_to_fasta.xml b/tools/fasta_tools/tabular_to_fasta.xml
index 639c5af3cd1..f0e2dd31ba2 100644
--- a/tools/fasta_tools/tabular_to_fasta.xml
+++ b/tools/fasta_tools/tabular_to_fasta.xml
@@ -25,10 +25,6 @@ Solexa data::
 
 	5	300	902	419	GACTCATGATTTCTTACCTATTAGTGGTTGAACATC
 	5	300	880	431	GTGATATGTATGTTGACGGCCATAAGGCTGCTTCTT
-	5	300	896	461	GTTGTCGATAGAACTTCATGTGCCTGTAAAACAAGT
-	5	300	890	751	ACCAACCAGAACGTGAAAAAGCGTCCTGCGTGTAGC
-	5	300	897	443	GTTTATGTTGGTTTCATGGTTTTGTCTAACTTTATC
-	5	300	906	879	GCTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCG
 	
 Selecting **c3 and c4** as the Title Columns and **c5** as the Sequence Column will result in::
 
@@ -36,14 +32,6 @@ Selecting **c3 and c4** as the Title Columns and **c5** as the Sequence Column w
 	GACTCATGATTTCTTACCTATTAGTGGTTGAACATC
 	&gt;880_431
 	GTGATATGTATGTTGACGGCCATAAGGCTGCTTCTT
-	&gt;896_461
-	GTTGTCGATAGAACTTCATGTGCCTGTAAAACAAGT
-	&gt;890_751
-	ACCAACCAGAACGTGAAAAAGCGTCCTGCGTGTAGC
-	&gt;897_443
-	GTTTATGTTGGTTTCATGGTTTTGTCTAACTTTATC
-	&gt;906_879
-	GCTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCG
 	
 	</help>
 </tool>
\ No newline at end of file
diff --git a/tools/metag_tools/short_reads_figure_score.xml b/tools/metag_tools/short_reads_figure_score.xml
index da9e183807a..8a13c5146b2 100644
--- a/tools/metag_tools/short_reads_figure_score.xml
+++ b/tools/metag_tools/short_reads_figure_score.xml
@@ -1,5 +1,5 @@
 <tool id="quality_score_distribution" name="Show Quality Score Distribution">
-<description>as a boxplot</description>
+<description></description>
 
 <command interpreter="python">short_reads_figure_score.py $input1 $output1 </command>
 
@@ -43,21 +43,13 @@ You can also upload your files in a zip file format and use this tool.
 
 454 data::
 
-	&gt;EYKX4VC01B65GS length=54 xy=0780_1755 region=1 run=R_2007_11_07_16_15_57_
-	23 33 34 25 28 28 28 32 23 34 27 4 28 28 31 21 28 27 27 28 28 28 28 28 28 28 33 23 28 33 
-	24 28 27 31 21 28 28 33 26 33 24 27 28 28 28 28 28 28 28 32 23 28 34 25
+	&gt;seq1
+	23 33 34 25 28 28 28 32 23 34 27 4 28 28 31 21 28
 
-Solexa data (36bp)::
+Solexa data::
 
  	-40  -40   40  -40	 -40  -40  -40   40	 -40  -40   40  -40	  40  -40  -40  -40	 -40  -40  -40   40	  
- 	40  -40  -40  -40	 -40  -40  -40   40	 -40  -40   40  -40	 -40  -40  -40   40	  40  -40  -40  -40	 
- 	-40  -40  -40   40	 -40  -40   40  -40	 -40  -40  -40   40	 -40  -40  -40   40	 -40  -40   40  -40	  
- 	40  -40  -40  -40	  -5    5  -40  -40	 -40  -40   40  -40	 -40  -40   40  -40	 -40   21  -40  -21	 
- 	-40   40  -40  -40	  40  -40  -40  -40	 -40  -40  -40   40	  40  -40  -40  -40	  12  -40  -40  -12	 
- 	-36  -40   36  -40	 -40  -40   40  -40	  -4    4  -40  -40	 -40  -40  -40   40	 -40  -40   14  -14	 
- 	-40   40  -40  -40	 -40  -40  -40   40	 -40  -40  -40   40	 -40   40  -40  -40	 -40  -40  -40   40	 
- 	-40  -40  -25   25
-
+ 
 boxplot::
 
     For showing purpose, this figure is not generated from the above examples.
diff --git a/tools/metag_tools/short_reads_trim_seq.xml b/tools/metag_tools/short_reads_trim_seq.xml
index 4155d04ddc3..e6f0d2b8fd0 100644
--- a/tools/metag_tools/short_reads_trim_seq.xml
+++ b/tools/metag_tools/short_reads_trim_seq.xml
@@ -75,65 +75,32 @@ If there are more than one substring, the tool outputs all of them in separated
 
 454 data::
 
-	&gt;EYKX4VC01B65GS length=54 xy=0784_1754 region=1 run=R_2007_11_07_16_15_57_
-	CCGGTATCCGGGTGCCGTGATGAGCGCCACCGGAACGAATTCGACTATGCCGAA
-	&gt;EYKX4VC01BNCSP length=187 xy=0558_3831 region=1 run=R_2007_11_07_16_15_57_
-	CTTACCGGTCACCACCGTGCCTTCAGGATTGATCGCCAGATCGGTCGGTGCGTCAGGCGG
-	GGTGACATCGCCCACCACGGTACTCACTGGCTGGCTCTGGTTCCCGGCGGCATCGGAGGC
-	CACCACGTTGAGGGTATTCCCCTCGGTTTGTGGCTCGGTGAGAACCACGTTGTAGTCGCC
-	ATTGGTC
+	&gt;seq1
+	CCGGTATCCG
 	
 454 quality score::
 
-	&gt;EYKX4VC01B65GS length=54 xy=0784_1754 region=1 run=R_2007_11_07_16_15_57_
-	33 23 34 25 28 28 28 32 23 34 27 4 28 28 31 21 28 27 27 28 28 28 28 28 28 28 33 23 28 33 
-	24 36 27 31 21 28 28 33 26 33 24 27 28 28 28 28 28 28 28 32 23 28 34 25
-	&gt;EYKX4VC01BNCSP length=187 xy=0558_3831 region=1 run=R_2007_11_07_16_15_57_
-	27 35 26 25 37 28 37 28 25 28 27 36 27 28 36 27 28 28 27 36 27 30 19 27 28 36 28 23 36 27 
-	27 28 27 27 28 37 29 27 26 27 24 24 36 27 26 28 36 28 24 25 21 28 24 28 26 34 25 26 43 36
-	22 9 23 19 28 28 28 28 26 28 39 32 12 27 36 28 28 26 37 28 28 26 28 28 28 27 28 26 36 27 
-	27 27 36 28 27 27 28 28 36 27 36 28 39 32 12 35 28 26 37 29 28 28 28 28 37 29 28 36 28 35
-	26 27 37 29 28 26 28 36 28 26 24 38 32 11 28 26 32 24 36 32 18 2 27 25 33 26 32 28 6 18 
-	22 26 17 15 14 28 20 8 22 21 14 22 26 16 26 16 28 20 22 27 18 27 18 27 28 27 20 25 34 27
-	27 33 25 34 28 8 26
+	&gt;seq1
+	33 19 34 25 28 28 28 32 15 34 
 
-454 Output::
+454 Output (trimmed by quality score 20 and returned the longest substring)::
 
-	&gt;EYKX4VC01BV9R8 length=54 xy=0660_2038 region=1 run=R_2007_11_07_16_15_57_
-	CTATTCAGCAGCACTGCGTT
-	&gt;EYKX4VC01BO0UO length=222 xy=0577_3838 region=1 run=R_2007_11_07_16_15_57_
-	CTGCAGTACCGCTTCTGGCTGCACTATGCCGAAGGCTCGCTGATGCCGCTGCTGTTAATGAAGCTGGTGTTCGCCAGCCTGG
+	&gt;seq1
+	GGTATC
 
 Solexa data::
 
-	5	300	902	419	GACTCATGATTTCTTACCTATTAGTGGTTGAACATC
-	5	300	880	431	GTGATATGTATGTTGACGGCCATAAGGCTGCTTCTT
+	5	300	902	419	TTCTTACCTATTAGTGGTTGAACATC
 
-Solexa quality score::
 
- 	-40  -40   40  -40	  40  -40  -40  -40	 -40   40  -40  -40	 -40  -40  -40   40	 -40   40  -40  -40	  
- 	40  -40  -40  -40	 -40  -40  -40   40	 -40  -40   40  -40	  40  -40  -40  -40	 -40  -40  -40   40	 
- 	-40  -40  -40   40	 -40  -40  -40   40	 -40   40  -40  -40	 -40  -40  -40   40	 -40  -40  -40   40	  
- 	40  -40  -40  -40	 -40   40  -40  -40	 -40   40  -40  -40	 -40  -40  -40   40	  40  -40  -40  -40	 
- 	-40  -40  -40   40	 -40  -40  -40   40	  40  -40  -40  -40	 -40  -40   40  -40	 -40  -40  -40   40	 
- 	-40  -40   40  -40	 -40  -40   40  -40	 -40  -40  -40   40	 -40  -40  -40   40	 -40  -40   40  -40	  
- 	40  -40  -40  -40	  40  -40  -40  -40	 -40   40  -40  -40	  40  -40  -40  -40	 -40  -40  -15   15	 
- 	-40   40  -40  -40
- 	-40  -40   40  -40	 -40  -40  -40   40	 -40  -40   40  -40	  40  -40  -40  -40	 -40  -40  -40   40	  
- 	40  -40  -40  -40	 -40  -40  -40   40	 -40  -40   40  -40	 -40  -40  -40   40	  40  -40  -40  -40	 
- 	-40  -40  -40   40	 -40  -40   40  -40	 -40  -40  -40   40	 -40  -40  -40   40	 -40  -40   40  -40	  
- 	40  -40  -40  -40	  -5    5  -40  -40	 -40  -40   40  -40	 -40  -40   40  -40	 -40   21  -40  -21	 
- 	-40   40  -40  -40	  40  -40  -40  -40	 -40  -40  -40   40	  40  -40  -40  -40	  12  -40  -40  -12	 
- 	-36  -40   36  -40	 -40  -40   40  -40	  -4    4  -40  -40	 -40  -40  -40   40	 -40  -40   14  -14	 
- 	-40   40  -40  -40	 -40  -40  -40   40	 -40  -40  -40   40	 -40   40  -40  -40	 -40  -40  -40   40	 
- 	-40  -40  -25   25
+Solexa quality score (only showed the maximum value)::
+	  
+ 	40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 15 40
 	
 Solexa Output::
 
 	&gt;15774
-	CTTATCAGAAACGGCAGAAGTGCCAGCCTGCAACGT
-	&gt;15775
-	ATTTGTCTAGGAAATAACCGTCAGGATTGACAC	
+	TTCTTACCTATTAGTGGTTGAACA
 	
 The fasta title will be replaced by a unique number in Solexa output.