opensource/galaxy
3
0
Fork 0
mirror of https://github.com/galaxyproject/galaxy.git synced 2026-09-24 16:30:27 +08:00
Code Issues Packages Projects Releases Wiki Activity

update several xml files for better help descriptions.

Browse Source 
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.
This commit is contained in:
Wen-Yu Chung
2008-02-05 18:32:42 +00:00
parent ee85154a15
commit f077afa436
7 changed files with 48 additions and 147 deletions
Download Patch File Download Diff File Expand all files Collapse all files
tool_conf.xml.sample
+2 -3
View File
@@ -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>
tools/fasta_tools/fasta_to_tabular.xml
+6 -9
View File
@@ -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>
tools/fasta_tools/fasta_tool_compute_length.xml
+10 -25
View File
@@ -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>
tools/fasta_tools/fasta_tool_filter_by_length.xml
+13 -40
View File
@@ -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>
tools/fasta_tools/tabular_to_fasta.xml
-12
View File
@@ -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>
tools/metag_tools/short_reads_figure_score.xml
+5 -13
View File
@@ -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.
tools/metag_tools/short_reads_trim_seq.xml
+12 -45
View File
@@ -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.