| Next changeset 1:d2d1d48c8e3e (2015-12-18) |
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Commit message:
planemo upload commit 870da8582a7bc43817b1de0720397ae60a8efef6-dirty |
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spolpred.sh spolpred.xml tool_dependencies.xml |
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| diff -r 000000000000 -r 5402893569cb spolpred.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/spolpred.sh Tue Dec 15 14:19:42 2015 -0500 |
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| @@ -0,0 +1,10 @@ +#/bin/bash + +name=$1 +shift + +spolpred $@ + +sed -i s/^.*\t/$name/ output.txt + +exit 0 |
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| diff -r 000000000000 -r 5402893569cb spolpred.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/spolpred.xml Tue Dec 15 14:19:42 2015 -0500 |
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| @@ -0,0 +1,148 @@ +<?xml version="1.0"?> +<tool id="spolpred" name="SpolPred" version="1.0.0"> + <description>with options and commands</description> + <requirements> + <requirement type="package" version="1.0.0">spolpred</requirement> + </requirements> + <command interpreter="bash"> + +#set $output=$input_file.name + +spolpred.sh "$input_file.name" $input_file + +-l $read_length -b $type_reads -d $more_details -s $screening_options.stop_screening + +#if $screening_options.stop_screening == "on": + -a $screening_options.screening_threshold +#end if + +-m $matching_threshold + + </command> + <inputs> + <param name="input_file" type="data" format="fastqsanger" label="FASTQ input file"/> + + <param name="read_length" type="integer" label="Read length [35, 1000]" value="75"> + <validator type="in_range" min="35" max="1000" message="Must be between 35 and 1000 (inclusive)"/> + </param> + + <param name="type_reads" type="select" label="Type of input reads"> + <option value="d">Direct</option> + <option value="r">Reverse</option> + </param> + + <param name="more_details" type="select" label="Level of processing output detail" + help="If set on, processing details are output to the job's STDOUT, including + number of processed reads and number of spacer sequences found"> + <option value="on">High</option> + <option value="off">Normal</option> + </param> + + <conditional name="screening_options"> + <param name="stop_screening" type="select" label="Read screening" + help="Used to end read processing when Screening Threshold is reached"> + <option value="on">Perform read screening</option> + <option value="off">Do not perform read screening</option> + </param> + <when value="on"> + <param name="screening_threshold" type="integer" label="Screening threshold" value="50" + help="Average number of spacer occurrences used to stop screening"> + <validator type="in_range" min="0" max="inf" message="Must be at least 0"/> + </param> + </when> + <when value="off"/> + </conditional> + + <param name="matching_threshold" type="integer" label="Matching threshold" value="4" + help="Minimum number of spacer occurrences below which spacer absence is assigned"> + <validator type="in_range" min="1" max="inf" message="Must be at least 1"/> + </param> + + </inputs> + <outputs> + <data name="outfile" format="tabular" from_work_dir="output.txt"/> + </outputs> + + <tests> + <test> + <param/> + <output/> + </test> + </tests> + +<help> + **Frequently Asked Questions** + + **SpolPred only accepts one FASTQ file, what if I have got paired-end reads?** + + Forward and reverse read files can be merged into one by making use of the Perl script + shuffleSequences_fastq.pl provided in Velvet software suite. SpolPred run will therefore take longer + than using only forward or reverse reads. In our dataset (read Methods for more details), the forward file + had enough reads to find all present spacers and infer the octal code for 49 out of 51 samples. That + decision will have to be made depending on the sample coverage depth. + + + + **What if I have a FASTA file?** + + SpolPred has been particularly designed to process raw reads and therefore only supports sequence + files in FASTQ format. + + + + **What is the point of stopping the read screening?** + + By default, all reads in the FASTQ file will be processed. Nevertheless, we have observed that a point is + reached when no more reads are needed to infer the octal code, in other words, the number of spacer + occurrences is high enough and steady to assume that all present spacers have already been found. + Therefore, stopping the program at this point would save time and computer resources. If low coverage + is the case, stopping the scanning is not advisable. + + + + **How do I choose the Screening threshold?** + + If you have decided to scan the whole input file there is no need to set such threshold. The Screening + threshold is used to let the program know when the screening should stop. Such value will depend on + read coverage. Running the software and looking at the number of times all spacers are detected will + provide insight into both the coverage and the most appropriate threshold value. + + + + **Why is a Matching threshold required? Are spacers not supposed to occur uniquely?** + + The number of times each spacer is found is tracked during the screening and absence assigned when + such number does not reach a user-defined threshold (4 times by default). This threshold, here called + Matching threshold, has had to be implemented because for some absent spacers, a few spurious + matches were found. Those false positives are likely to be related with bad-quality issues, like + sequencing errors. In our data set, no more than 3 false matches were detected for absent spacers, in + contrast to 50-150 found per present spacer. + + + + **Should I be worried then about false positive matches?** + + As long as proper pre-filtering steps are carried out to the raw reads, no important issues are expected + to come up. + + + + **Can I change the number of allowed SNPs when querying the spacers?** + + This option has not been implemented. Spacer sequences are conserved and only one SNP has been + reported to occur at the most. + + + + **Why are exact matches output as well?** + + The number of read-spacer exact matches, i.e. without allowing SNPs, will enable the easily + identification of SNPs on spacer sequences. When inferring the octal code, exact matches are not + employed. + + Wrapper Author: Mark Iskander +</help> +<citations> + <citation type="doi">10.1093/bioinformatics/bts544</citation> +</citations> +</tool> |
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| diff -r 000000000000 -r 5402893569cb tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Tue Dec 15 14:19:42 2015 -0500 |
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| @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="spolpred" version="1.0.0"> + <repository changeset_revision="bb26e23d7178" name="package_spolpred_1_0_0" owner="nml" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency> |