# HG changeset patch
# User joachim-jacob
# Date 1360662647 18000
# Node ID 9537dd9dd18b240c262952ff36f2003842e6157a
# Parent  934cd08c77af0beec15b06b79cf06ee0bc0cf8c5
Uploaded

diff -r 934cd08c77af -r 9537dd9dd18b bamqc.xml
--- a/bamqc.xml	Tue Feb 12 04:48:36 2013 -0500
+++ b/bamqc.xml	Tue Feb 12 04:50:47 2013 -0500
@@ -69,170 +69,17 @@
     </configfiles> 
 
     <tests>
-        <!-- Test base-space single-end reads with pre-built index and preset parameters -->
-        <test>
-            <!-- TopHat commands:
-            tophat -o tmp_dir -p 1 tophat_in1 test-data/tophat_in2.fastqsanger
-            Rename the files in tmp_dir appropriately
-            -->
-            <param name="input1" ftype="fastqsanger" value="tophat_in2.fastqsanger" />
-            <param name="genomeSource" value="indexed" />
-            <param name="index" value="tophat_test" />
-            <param name="sPaired" value="single" />
-            <param name="sSettingsType" value="preSet" />
-            <output name="junctions" file="tophat_out1j.bed" />
-            <output name="accepted_hits" file="tophat_out1h.bam" compare="sim_size" />
-        </test>
-        <!-- Test using base-space test data: paired-end reads, index from history. -->
-        <test>
-            <!-- TopHat commands:
-            bowtie-build -f test-data/tophat_in1.fasta tophat_in1
-            tophat -o tmp_dir -p 1 -r 20 tophat_in1 test-data/tophat_in2.fastqsanger test-data/tophat_in3.fastqsanger
-            Rename the files in tmp_dir appropriately
-            -->
-            <param name="input1" ftype="fastqsanger" value="tophat_in2.fastqsanger" />
-            <param name="genomeSource" value="history" />
-            <param name="ownFile" ftype="fasta" value="tophat_in1.fasta" />
-            <param name="sPaired" value="paired" />
-            <param name="input2" ftype="fastqsanger" value="tophat_in3.fastqsanger" />
-            <param name="mate_inner_distance" value="20" />
-            <param name="pSettingsType" value="preSet" />
-            <output name="junctions" file="tophat_out2j.bed" />
-            <output name="accepted_hits" file="tophat_out2h.bam" compare="sim_size" />
-        </test>
-        <!-- Test base-space single-end reads with user-supplied reference fasta and full parameters -->
-        <test>
-            <!-- Tophat commands:
-            bowtie-build -f test-data/tophat_in1.fasta tophat_in1
-            tophat -o tmp_dir -p 1 -a 8 -m 0 -i 70 -I 500000 -F 0.15 -g 40 +coverage-search +min-coverage-intron 50 +max-coverage-intro 20000 +segment-mismatches 2 +segment-length 25 +closure-search +min-closure-exon 50 +min-closure-intron 50 +max-closure-intro 5000 +microexon-search tophat_in1 test-data/tophat_in2.fastqsanger
-            Replace the + with double-dash
-            Rename the files in tmp_dir appropriately
-            -->
-            <param name="input1" ftype="fastqsanger" value="tophat_in2.fastqsanger"/>
-            <param name="genomeSource" value="history"/>
-            <param name="ownFile" value="tophat_in1.fasta"/>
-            <param name="sPaired" value="single"/>
-            <param name="sSettingsType" value="full"/>
-            <param name="library_type" value="FR Unstranded"/>
-            <param name="anchor_length" value="8"/>
-            <param name="splice_mismatches" value="0"/>
-            <param name="min_intron_length" value="70"/>
-            <param name="max_intron_length" value="500000"/>
-            <param name="max_multihits" value="40"/>
-            <param name="min_segment_intron" value="50" />
-            <param name="max_segment_intron" value="500000" />
-            <param name="seg_mismatches" value="2"/>
-            <param name="seg_length" value="25"/>
-            <param name="allow_indel_search" value="Yes"/>
-            <param name="max_insertion_length" value="3"/>
-            <param name="max_deletion_length" value="3"/>
-            <param name="use_junctions" value="Yes" />
-            <param name="use_annotations" value="No" />
-            <param name="use_juncs" value="No" />
-            <param name="no_novel_juncs" value="No" />
-            <param name="use_search" value="Yes" />
-            <param name="min_closure_exon" value="50" />
-            <param name="min_closure_intron" value="50" />
-            <param name="max_closure_intron" value="5000" />
-            <param name="use_search" value="Yes" />
-            <param name="min_coverage_intron" value="50" />
-            <param name="max_coverage_intron" value="20000" />
-            <param name="microexon_search" value="Yes" />
-            <output name="insertions" file="tophat_out3i.bed" />
-            <output name="deletions" file="tophat_out3d.bed" />
-            <output name="junctions" file="tophat_out3j.bed" />
-            <output name="accepted_hits" file="tophat_out3h.bam" compare="sim_size" />
-        </test>
-        <!-- Test base-space paired-end reads with user-supplied reference fasta and full parameters -->
-        <test>
-            <!-- TopHat commands:
-            tophat -o tmp_dir -r 20 -p 1 -a 8 -m 0 -i 70 -I 500000 -F 0.15 -g 40 +coverage-search +min-coverage-intron 50 +max-coverage-intro 20000 +segment-mismatches 2 +segment-length 25 +microexon-search tophat_in1 test-data/tophat_in2.fastqsanger test-data/tophat_in3.fastqsanger
-            Replace the + with double-dash
-            Rename the files in tmp_dir appropriately
-            -->
-            <param name="input1" ftype="fastqsanger" value="tophat_in2.fastqsanger"/>
-            <param name="genomeSource" value="indexed"/>
-            <param name="index" value="tophat_test"/>
-            <param name="sPaired" value="paired"/>
-            <param name="input2" ftype="fastqsanger" value="tophat_in3.fastqsanger"/>
-            <param name="mate_inner_distance" value="20"/>
-            <param name="pSettingsType" value="full"/>
-            <param name="library_type" value="FR Unstranded"/>
-            <param name="mate_std_dev" value="20"/>
-            <param name="anchor_length" value="8"/>
-            <param name="splice_mismatches" value="0"/>
-            <param name="min_intron_length" value="70"/>
-            <param name="max_intron_length" value="500000"/>
-            <param name="max_multihits" value="40"/>
-            <param name="min_segment_intron" value="50" />
-            <param name="max_segment_intron" value="500000" />
-            <param name="seg_mismatches" value="2"/>
-            <param name="seg_length" value="25"/>
-            <param name="allow_indel_search" value="No"/>
-            <param name="use_junctions" value="Yes" />
-            <param name="use_annotations" value="No" />
-            <param name="use_juncs" value="No" />
-            <param name="no_novel_juncs" value="No" />
-            <param name="use_search" value="No" />
-            <param name="microexon_search" value="Yes" />
-            <output name="junctions" file="tophat_out4j.bed" />
-            <output name="accepted_hits" file="tophat_out4h.bam" compare="sim_size" />
-        </test>
     </tests>
 
     <help>
 **Tool Overview**
 
-Tool_ allows for simply but throroughly checking of the quality of mapping. 
+Bamqc_ allows for simply but throroughly checking of the quality of mapping. 
 
-.. _Tool: http://qualimap.bioinfo.cipf.es//
+.. _Bamqc: http://qualimap.bioinfo.cipf.es//
         
 ------
 
-**Know what you are doing**
-
-.. class:: warningmark
-
-Know what you are doing by reading the `documentation`__ and experimenting. 
-
-.. __: http://tophat.cbcb.umd.edu/manual.html
-
-------
-
-**Input formats**
-
-Tool accepts files in Sanger FASTQ format. Use the FASTQ Groomer to prepare your files.
-
-------
-
-**Outputs**
-
-Tool produces two output files:
-
-- junctions -- A UCSC BED_ track of junctions reported by TopHat. Each junction consists of two connected BED blocks, where each block is as long as the maximal overhang of any read spanning the junction. The score is the number of alignments spanning the junction.
-- accepted_hits -- A list of read alignments in BAM_ format.
-
-.. _BED: http://genome.ucsc.edu/FAQ/FAQformat.html#format1
-.. _BAM: http://samtools.sourceforge.net/
-
-Two other possible outputs, depending on the options you choose, are insertions and deletions, both of which are in BED format.
-
--------
-
-**Tool settings**
-
-All of the options have a default value. You can change any of them. Some of the options in Tophat have been implemented here.
-
-------
-
-**Tool parameter list**
-
-This is a list of implemented Tophat options::
-
-  -r                                This is the expected (mean) inner distance between mate pairs. For, example, for paired end runs with fragments 
-                                    selected at 300bp, where each end is 50bp, you should set -r to be 200. There is no default, and this parameter 
-                                    is required for paired end runs.
-
     </help>
 </tool>