Mercurial > repos > stef > falco
changeset 90:07c810e4061c draft
Uploaded
| author | stef |
|---|---|
| date | Fri, 17 Jul 2015 06:53:45 -0400 |
| parents | cf271f328d5e |
| children | 3141d9f20025 |
| files | falco-call.sh falco-call.xml falco-filter-report.xml tool-data/HCT116_test_ABL1.bam tool-data/HCT116_test_ABL1.bam.bai |
| diffstat | 5 files changed, 58 insertions(+), 47 deletions(-) [+] |
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--- a/falco-call.sh Fri Jul 17 06:02:36 2015 -0400 +++ b/falco-call.sh Fri Jul 17 06:53:45 2015 -0400 @@ -40,6 +40,15 @@ #bam_base=`echo $bam_name | sed 's#.bam$##' - ` bam_base=$job_name +## in case of test run (re)set params +if [[ $test_run == 'true' ]] +then + MANIFEST_PARAM="" + FILTER_PARAM="" + bam_file=$TOOLDIR/tool-data/HCT116_test_ABL1.bam + #bam_base="GALAXY-FALCO-TEST" +fi + ## ---------- ## Status / debug ## ---------- @@ -47,11 +56,11 @@ if [ $DEBUG ] then DBS="[INFO] " - echo $DBS"FILTER: "$filter_file + echo $DBS"FILTER: "$filter_file echo $DBS"MANIFEST: "$manifest_file echo $DBS"REF FILE: "$REF_FILE - echo $DBS"DB KEY: "$DB_KEY - echo $DBS"REF SRC: "$REF_SOURCE + echo $DBS"DB KEY: "$DB_KEY + echo $DBS"REF SRC: "$REF_SOURCE echo $DBS"BAM FILE: "$bam_file echo $DBS"BAM NAME: "$bam_name echo $DBS"BAM BASE: "$bam_base @@ -89,7 +98,7 @@ echo "</head>" >> $html_out echo "<body>" >> $html_out echo " <h1>FALCO</h1>" >> $html_out -echo " <p>This page is way to get output files that are not implemented in galaxy history, it is not intended to be a user-friendly way of displaying anything ;)</p>" >> $html_out +echo " <p>This page is way to get output files that are not implemented in galaxy history, it is not intended to be a user-friendly way of displaying anything ;)</p><p>Also not all files might have been copied. To delete this files below from the galaxy installation delete the html page in your history.." >> $html_out #echo " <a href=\"index.html\">HTML</a>" >> $html_out echo " <table><tbody>" >> $html_out for file in *.vcf *.txt *stderr *stdout @@ -107,7 +116,7 @@ ## creating galaxy history outputs ## ---------- #cp 'index.html' $html_out # this is the overview of samples html -#cp $bam_base'.html' $out_path/'out.html' # this is the sample html +cp $bam_base'.html' $out_path/'out.html' # this is the sample html cp $bam_base'.falco.vcf' $vcf_out cp $bam_base'.qc.ann.qual.txt' $qc_ann_qual_out cp $bam_base'.qc2.ann.txt' $qc2_ann_txt_out @@ -118,7 +127,9 @@ ## ---------- #cp -r ./$bam_base/*png $out_path/$bam_base/ #cp -r ./* $out_path -cp *.vcf $out_path; cp *.txt $out_path; cp *_std* $out_path +cp *.vcf $out_path; +#cp *.txt $out_path; +cp *_std* $out_path ## ---------- echo "END falco sh"
--- a/falco-call.xml Fri Jul 17 06:02:36 2015 -0400 +++ b/falco-call.xml Fri Jul 17 06:53:45 2015 -0400 @@ -23,6 +23,11 @@ <!-- ==================== --> <!-- General inputs --> <!-- ==================== --> + <param name="jobName" type="text" optional="false" label="Analysis/ouput name" help="Supply a name for the outputs to remind you what they contain. The string entered here will also be the sample-name in the VCF" value="TEST"> + <validator type="empty_field" /> + <validator type="regex" message="This field may contain only non-whitespace characters">\S+</validator> + </param> + <conditional name="genomeSource"> <param name="refGenomeSource" type="select" label="You can select a reference genome from your history or use a built-in index"> <option value="indexed">Use a built-in index</option> @@ -41,18 +46,26 @@ </when> </conditional> - <param name="jobName" type="text" optional="false" label="Analysis/ouput name" help="Supply a name for the outputs to remind you what they contain" value="TEST"> - <validator type="empty_field" /> - <validator type="regex" message="This field may contain only non-whitespace characters">\S+</validator> - </param> <param name="bam" type="data" multiple="false" optional="false" format="bam" label="Input BAM" help="Select BAM file" /> - <param format="tabular" name="filter_file" optional="True" type="data" label="FILTER File" help="When left empty, default list of genomic positions is used"/> - <param format="txt" name="manifest_file" optional="True" type="data" label="MANIFEST File" help="When left empty, default Cancer Panel is used"/> + <param format="tabular" name="filter_file" optional="True" type="data" label="FILTER File" help="When left empty, built-in list of genomic positions is used"/> + <param format="txt" name="manifest_file" optional="True" type="data" label="MANIFEST File" help="When left empty, built-in panel is used (TruSeq Amplicon Cancer Panel)"/> <!-- ==================== --> - <!-- Option to use your own bin annotations --> + <!-- Optional hisotry output: copynumber TXT file --> <!-- ==================== --> + <param name="txt2history" type="select" label="Also output falco specific TXT files to history" help="These text files are much larger but are required for the falco-report tool, so usually you only want these in a workflow and auto-delete them at the end"> + <option value="false">no</option> + <option value="true">yes</option> + </param> + + <!-- ==================== --> + <!-- Option to perform a test run with built in data --> + <!-- ==================== --> + <param name="testRun" type="select" label="Run with test data" help="Use built-in HCT116 data instead of input BAMs. This dataset contains only one amplicon."> + <option value="false">no</option> + <option value="true">yes</option> + </param> </inputs> @@ -70,6 +83,8 @@ qc_ann_qual_out=$qc_ann_qual_output qc2_ann_txt_out=$qc2_ann_txt_output qc_targets_txt_out=$qc_targets_txt_output + also_output_txt=$txt2history + test_run=$testRun out_path=${html_output.files_path} job_name=$jobName @@ -90,11 +105,19 @@ <!-- Main output is an html based report, additional on request --> <!-- ==================== --> <outputs> - <data format="html" name="html_output" label="FALCO-calling (${jobName})" /> + <data format="html" name="html_output" label="FALCO-calling (${jobName})"> + <filter>(txt2history == 'true')</filter> + </data> <data format="vcf" name="vcf_output" label="FALCO-calling (${jobName}): VCF" /> - <data format="tabular" name="qc_ann_qual_output" label="FALCO-calling (${jobName}): qc_ann_qual" /> - <data format="tabular" name="qc2_ann_txt_output" label="FALCO-calling (${jobName}): qc2_ann" /> - <data format="tabular" name="qc_targets_txt_output" label="FALCO-calling (${jobName}): qc_targets" /> + <data format="tabular" name="qc_ann_qual_output" label="FALCO-calling (${jobName}): qc_ann_qual"> + <filter>(txt2history == 'true')</filter> + </data> + <data format="tabular" name="qc2_ann_txt_output" label="FALCO-calling (${jobName}): qc2_ann"> + <filter>(txt2history == 'true')</filter> + </data> + <data format="tabular" name="qc_targets_txt_output" label="FALCO-calling (${jobName}): qc_targets"> + <filter>(txt2history == 'true')</filter> + </data> </outputs> <!-- ==================== --> @@ -123,13 +146,13 @@ **Notes** -Because each amplicon is considered separate test, if two amplicons overlap this can cause the same variant position to be present twice in the output VCF. This is intentional, you can use this to evaluate the quality of the variant call beyond the amplicon. +Because each amplicon is analysed separately, when two amplicons overlap this can cause the same variant position to be present twice in the output VCF. This is intentional, you can use this to evaluate the quality of the variant call beyond the amplicon reads. ----- **Citation** -For the underlying tool please cite: Daoud Sie et al. Performance of amplicon-based next generation DNA sequencing for diagnostic gene mutation profiling in oncopathology (Cell Oncol 2014 Oct;37(5):353-61). [Pubmed] +For the underlying tool please cite: Daoud Sie et al. Performance of amplicon-based next generation DNA sequencing for diagnostic gene mutation profiling in oncopathology (Cell Oncol 2014 Oct;37(5):353-61). Pubmed_ .. _Pubmed: http://www.ncbi.nlm.nih.gov/pubmed/25209392
--- a/falco-filter-report.xml Fri Jul 17 06:02:36 2015 -0400 +++ b/falco-filter-report.xml Fri Jul 17 06:53:45 2015 -0400 @@ -20,41 +20,18 @@ </stdio> <inputs> - <!-- ==================== --> - <!-- General inputs --> - <!-- ==================== --> - <!-- <conditional name="genomeSource"> - <param name="refGenomeSource" type="select" label="You can select a reference genome from your history or use a built-in index"> - <option value="indexed">Use a built-in index</option> - <option value="history">Use one from history</option> - </param> - <when value="indexed"> - <param name="indices" type="select" label="Select a reference genome"> - <options from_data_table="all_fasta"> - <filter type="sort_by" column="2" /> - <validator type="no_options" message="No indexes are available in table" /> - </options> - </param> - </when> - <when value="history"> - <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" /> - </when> - </conditional> --> <param name="jobName" type="text" optional="false" label="Analysis/ouput name" help="Supply a name for the outputs to remind you what they contain" value="TEST"> <validator type="empty_field" /> <validator type="regex" message="This field may contain only non-whitespace characters">\S+</validator> </param> + <param name="vcf" type="data" multiple="false" optional="false" format="vcf" label="Input VCF" help="NOTE VCF must be annotated with SNPEFF (should contain EFF FIELD)" /> <param name="vcf2" type="data" multiple="false" optional="true" format="vcf" label="Input VCF (optional second VCF)" help="NOTE VCF must be annotated with SNPEFF (should contain EFF FIELD)" /> - <param format="tabular" name="qc_ann_qual" optional="false" type="data" label="qc_ann_qual file" help="This file is output of the FALCO variant caller"/> - <param format="tabular" name="qc2_ann_txt" optional="false" type="data" label="qc2_ann_txt file" help="This file is output of the FALCO variant caller"/> - <param format="tabular" name="qc_targets_txt" optional="false" type="data" label="qc_targets_txt file" help="This file is output of the FALCO variant caller"/> - - <!-- ==================== --> - <!-- Option to use your own bin annotations --> - <!-- ==================== --> + <param format="tabular" name="qc_ann_qual" optional="false" type="data" label="qc_ann_qual file" help="This file is output of the FALCO variant caller falco-call"/> + <param format="tabular" name="qc2_ann_txt" optional="false" type="data" label="qc2_ann_txt file" help="This file is output of the FALCO variant caller fal-call"/> + <param format="tabular" name="qc_targets_txt" optional="false" type="data" label="qc_targets_txt file" help="Tabular text file with information about the amplicon regions. This file is output of the FALCO variant caller falco-call"/> </inputs> @@ -113,7 +90,7 @@ **Notes** -Because each amplicon is considered separate test, if two amplicons overlap this can cause the same variant position to be present twice in the output VCF. This is intentional, you can use this to evaluate the quality of the variant call beyond the amplicon. +Because each amplicon is analysed separately, when two amplicons overlap this can cause the same variant position to be present twice in the output VCF. This is intentional, you can use this to evaluate the quality of the variant call beyond the amplicon reads. -----