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snvphyl-galaxy
Commit 20811bd3 authored by Takadonet's avatar Takadonet
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removing old tool wrapper that is not used anymore

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tools/smalt_collection/smalt/smalt_check.sh deleted 100644 → 0
View file @ ce96cb25
#/bin/bash
#determine if we were given 1 or 2 fastq files
if [ $# -eq 3 ] || [ $# -eq 2 ]; then
#get the output file name
output=$1
#remove it from the arguments list
shift
$SMALT/smalt check $@ > $output
#remove header file
sed -i -e "1d" $output
else
#unknown arguments given
exit 1
fi
exit 0
tools/smalt_collection/smalt/smalt_check.xml deleted 100644 → 0
View file @ ce96cb25
<tool id="smalt_check" name="smalt check" version="0.0.3" >
<requirements>
<requirement type="package" version="1.1">smalt</requirement>
</requirements>
<command interpreter="bash">
smalt_check.sh $output
#if $singlePaired.sPaired == "single":
$singlePaired.sInput1
#elif $singlePaired.sPaired == "paired":
$singlePaired.pInput1 $singlePaired.pInput2
#elif $singlePaired.sPaired == "matePairs":
$singlePaired.mInput1 $singlePaired.mInput2
#end if
</command>
<description>Determine number of reads in fastq(s) and if they are mate-pair</description>
<inputs>
<conditional name="singlePaired">
<param name="sPaired" type="select" label="Is this library mate-paired?">
<option value="single">Single-end</option>
<option value="paired">Paired-end</option>
<option value="matePairs">MatePairs</option>
</param>
<when value="single">
<param name="sInput1" type="data" format="fastq" label="Single end illumina fastq file" optional="false"/>
</when>
<when value="paired">
<param name="pInput1" type="data" format="fastq,fastqsanger,fastqillumina,fastqsolexa" label="Forward FASTQ file" help="Must have ASCII encoded quality scores"/>
<param name="pInput2" type="data" format="fastq,fastqsanger,fastqillumina,fastqsolexa" label="Reverse FASTQ file" help="File format must match the Forward FASTQ file"/>
</when>
<when value="matePairs">
<param name="mInput1" type="data" format="fastq,fastqsanger,fastqillumina,fastqsolexa" label="Forward FASTQ file" help="Must have ASCII encoded quality scores"/>
<param name="mInput2" type="data" format="fastq,fastqsanger,fastqillumina,fastqsolexa" label="Reverse FASTQ file" help="File format must match the Forward FASTQ file"/>
</when>
</conditional>
</inputs>
<outputs>
<data format="tabular" name="output" />
</outputs>
<stdio>
<exit_code range="1" level="fatal" description="Unknown argument given." />
<exit_code range="2:" level="fatal" description="Unknown error." />
</stdio>
<help>
**What it does**
Check FASTA/FASTQ read files. If &#060;mate_file&#062; is specified, the reads are in pairs.
------
Please cite the website "http://www.sanger.ac.uk/resources/software/smalt/".
</help>
</tool>
tools/smalt_collection/smalt/smalt_index.xml deleted 100644 → 0
View file @ ce96cb25
<tool id="smalt_index" name="smalt index" version="0.0.3">
<requirements>
<requirement type="package" version="1.1">smalt</requirement>
</requirements>
<command>
/\$SMALT/smalt index
#if $k:
-k "$k"
#end if
#if $s:
-s "$s"
#end if
'temp' "$reference"
</command>
<description>Index a reference </description>
<inputs>
<param name="reference" type="data" format="fasta" label="Fasta reference file"/>
<param name="k" type="integer" value="13" label="K-mer size" help="Specifies the word length. [wordlen] is an integer within the limits. between 2 and less then 20. The default word length is 13"/>
<param name="s" type="text" label="Stepsiz" help="Specifies how many bases are skipped between indexed words."/>
</inputs>
<outputs>
<data name="output" label="SMI" from_work_dir="temp.smi"/>
<data name="output2" label="SMA" from_work_dir="temp.sma"/>
</outputs>
<stdio>
<exit_code range="1:" level="fatal" description="Unknown error" />
</stdio>
<help>
**What it does**
Generates an index of k-mer words for the genomic reference sequences. The words are of fixed length &#060;wordlen&#062; and are sampled at equidistant steps &#060;stepsiz&#062; bases apart. The reference sequences are provided in a single file &#060;reference_file&#062; in FASTA or FASTQ format. Two binary files are output. The file &#060;index_name&#062;.sma contains the reference sequences in compressed form. The file &#060;index_name&#062;.smi contains the k-mer word index.
------
Please cite the website "http://www.sanger.ac.uk/resources/software/smalt/".
------
-k &#060;wordlen&#062;
Specifies the word length. &#060;wordlen&#062; is an integer within the limits
2 &#060; wordlen &#060;= 20. The default word length is 13.
-s &#060;stepsiz&#062;
Specifies how many bases are skipped between indexed words. With '-s 1'
every k-mer word along the reference sequences is indexed. With '-s 2'
every other word is indexed etc. By default the step size is set equal
to the word length (tiling words).
</help>
</tool>
tools/smalt_collection/smalt/smalt_map.sh deleted 100644 → 0
View file @ ce96cb25
#/bin/bash
smi=$1
shift
sma=$1
shift
#get working directory so we can find the output files
CUR_DIR=`pwd`
cp "$smi" "$CUR_DIR/temp.smi"
cp "$sma" "$CUR_DIR/temp.sma"
#determine if we have 1 or 2
num_inputs=$1
shift
inputs=()
#determine how many fasta/fastq were given. Needs to be provided by user
if [ $num_inputs -eq 1 ]; then
inputs+=$1
shift
elif [ $num_inputs -eq 2 ]; then
inputs+=$1
shift
inputs+=' '
inputs+=$1
shift
else
exit 1
fi
$SMALT/smalt map $@ 'temp' $inputs
#remove index files
rm "$CUR_DIR/temp.smi"
rm "$CUR_DIR/temp.sma"
exit 0
tools/smalt_collection/smalt/smalt_map.xml deleted 100644 → 0
View file @ ce96cb25
This diff is collapsed.
tools/smalt_collection/smalt/smalt_sample.sh deleted 100644 → 0
View file @ ce96cb25
#/bin/bash
smi=$1
shift
sma=$1
shift
#get working directory so we can find the output files
CUR_DIR=`pwd`
cp "$smi" "$CUR_DIR/temp.smi"
cp "$sma" "$CUR_DIR/temp.sma"
#determine if we have 1 or 2
num_inputs=$1
shift
inputs=()
#determine how many fasta/fastq were given. Needs to be provided by user
if [ $num_inputs -eq 1 ]; then
inputs+=$1
shift
elif [ $num_inputs -eq 2 ]; then
inputs+=$1
shift
inputs+=' '
inputs+=$1
shift
else
exit 1
fi
$SMALT/smalt sample $@ 'temp' $inputs
#remove index files
rm "$CUR_DIR/temp.smi"
rm "$CUR_DIR/temp.sma"
exit 0
tools/smalt_collection/smalt/smalt_sample.xml deleted 100644 → 0
View file @ ce96cb25
<tool id="smalt_sample" name="smalt sample" version="0.0.3" >
<requirements>
<requirement type="package" version="1.1">smalt</requirement>
</requirements>
<command interpreter="bash">
smalt_sample.sh "$smi" "$sma"
2 "$mInput1" "$mInput2"
-o "$output"
#if $threads:
-n "$threads"
#end if
#if $minscor:
-m "$minscor"
#end if
#if $minbasq:
-q "$minbasq"
#end if
#if $num_reads:
-u "$num_reads"
#end if
</command>
<description>Sample insert size distribution for paired reads.</description>
<inputs>
<param name="mInput1" type="data" format="fastq,fastqsanger,fastqillumina,fastqsolexa" label="Forward FASTQ file" help="Must have ASCII encoded quality scores"/>
<param name="mInput2" type="data" format="fastq,fastqsanger,fastqillumina,fastqsolexa" label="Reverse FASTQ file" help="File format must match the Forward FASTQ file"/>
<param name="smi" type="data" label="SMI index" help=""/>
<param name="sma" type="data" label="SMA index" help=""/>
<param name="threads" type="text" format="integer" value="2" label="Number of threads to use" help="The order of the reads in the input files is not preserved for the output unless '-O' is also specified"/>
<param name="minscor" type="text" label="Sets an absolute threshold of the Smith-Waterman scores." help="Mappings with scores below that threshold will not be reported. The default is &#060; minscor &#062; = &#060; wordlen &#062; + &#060; stepsiz &#062; - 1"/>
<param name="minbasq" type="text" label="Sets a base quality threshold (0 &#060;= minbasq &#060;= 10, default 0)" help="K-mer words of the read with nucleotides that have a base quality below this threshold are not looked up in the hash index."/>
<param name="num_reads" type="integer" value="100" label="Map only every [num_reads]-th read pair" help="Default 100"/>
</inputs>
<outputs>
<data format="cigar" name="output" />
</outputs>
<stdio>
<exit_code range="1:" level="fatal" description="Unknown error" />
</stdio>
<help>
**What it does**
Sample insert size distribution for paired reads. A subset of the read
pairs is aligned with a reference in order to derrive the distribution of
insert sizes. The reference sequences and index are read from the files
[index_name.sma and [index_name].smi created by the 'index' task
------
Please cite the website "http://www.sanger.ac.uk/resources/software/smalt/".
</help>
</tool>
tools/smalt_collection/tool_conf.xml deleted 100644 → 0
View file @ ce96cb25
<?xml version="1.0"?>
<toolbox>
<section name="Smalt Tools" id="smalt">
<label text="Smalt Tools" id="smalt_tools" />
<tool file="smalt/tools/smalt/smalt_check.xml" />
<tool file="smalt/tools/smalt/smalt_index.xml" />
</section>
</toolbox>
tools/smalt_collection/tool_dependencies.xml deleted 100644 → 0
View file @ ce96cb25
<?xml version="1.0"?>
<tool_dependency>
<package name="smalt" version="1.1">
<install version="1.0">
<actions>
<action type="download_by_url" target_filename="smalt-0.7.5.tar.gz">http://downloads.sourceforge.net/project/smalt/smalt-0.7.5.tar.gz</action>
<action type="shell_command">./configure --prefix=$INSTALL_DIR</action>
<action type="make_install"></action>
<action type="set_environment">
<environment_variable name="SMALT" action="set_to">$INSTALL_DIR/bin</environment_variable>
<environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/share</environment_variable>
</action>
</actions>
</install>
<readme>
</readme>
</package>
</tool_dependency>
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