changeset 1:422485508110 draft

Uploaded
author petr-novak
date Fri, 24 Jul 2020 07:26:07 -0400
parents 43c4250c6761
children 349b197133dc
files repex_full_clustering.xml repex_tarean.xml tool_dependencies.xml
diffstat 3 files changed, 26 insertions(+), 565 deletions(-) [+]
line wrap: on
line diff
--- a/repex_full_clustering.xml	Thu Apr 30 07:42:45 2020 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,307 +0,0 @@
-<tool id="repeatexplorer2" name="RepeatExplorer2 clustering: " version="2.3.8" >
-    <stdio>
-      <regex match="lastdb: can't open file: NEAR" source="stderr" level="fatal" description="Version of last is too old, use ver 956 or higher\n" />
-      <regex match="Traceback" source="stderr" level="fatal" description="Unknown error" />
-      <regex match="error" source="stderr" level="fatal" description="Unknown error" />
-      <regex match="Warning" source="stderr" level="warning" description="Unknown error" />
-      <exit_code range="1:" level="fatal" description="Error" />
-    </stdio>
-    <description>Improved version or repeat discovery and characterization using graph-based sequence clustering</description>
-   <requirements>
-     <requirement type="package">last</requirement>
-     <requirement type="package">imagemagick</requirement>
-     <requirement type="package">mafft</requirement>
-     <requirement type="package">blast</requirement>
-     <requirement type="package" version="0.9.29" >diamond</requirement>
-     <requirement type="package">blast-legacy</requirement>
-     <requirement type="package">r-igraph</requirement>
-     <requirement type="package">r-data.tree</requirement>
-     <requirement type="package">r-stringr</requirement>
-     <requirement type="package">r-r2html</requirement>
-     <requirement type="package">r-hwriter</requirement>
-     <requirement type="package">r-dt</requirement>
-     <requirement type="package">r-scales</requirement>
-     <requirement type="package">r-plotrix</requirement>
-     <requirement type="package">r-png</requirement>
-     <requirement type="package">r-plyr</requirement>
-     <requirement type="package">r-dplyr</requirement>
-     <requirement type="package">r-optparse</requirement>
-     <requirement type="package">r-dbi</requirement>
-     <requirement type="package">r-rsqlite</requirement>
-     <requirement type="package">r-rserve</requirement>
-     <requirement type="package">bioconductor-biostrings</requirement>
-     <requirement type="package" version="2.3.8">repex_tarean_testing</requirement>
-     <requirement type="set_environment">REPEX</requirement>
-     <requirement type="set_environment">REPEX_VERSION</requirement>
-     <requirement type="package" version="0.9.1" >pyrserve</requirement>
-   </requirements>
-    <command >
-      export PYTHONHASHSEED=0;
-      \${REPEX}/seqclust --sample ${read_sampling.sample} --output_dir=tarean_output --logfile=${log} --cleanup $paired --taxon $taxon
-
-      #if $advanced_options.advanced:
-      --mincl $advanced_options.size_threshold $advanced_options.keep_names $advanced_options.automatic_filtering  -D $advanced_options.blastx.options_blastx
-      --assembly_min $advanced_options.assembly_min_cluster_size
-
-        #if $advanced_options.comparative.options_comparative:
-          --prefix_length $advanced_options.comparative.prefix_length
-        #end if
-      
-        #if $advanced_options.custom_library.options_custom_library:
-       	  -d $advanced_options.custom_library.library extra_database
-        #end if
-        
-        #if $advanced_options.options.options:
-         -opt $advanced_options.options.options
-        #end if 
-      #end if
-      ${FastaFile}  >stdout.log 2> stderr.log ;
-      echo "STDOUT CONTENT:" >> ${log} ;
-      cat stdout.log >> ${log} ;
-      echo "STDERR CONTENT:" >> ${log};
-      cat stderr.log >> ${log} &amp;&amp;
-      \${REPEX}/stderr_filter.py stderr.log &amp;&amp;
-      cd tarean_output &amp;&amp;
-      zip -r  ${ReportArchive}.zip * &amp;&amp;
-      mv ${ReportArchive}.zip ${ReportArchive} &amp;&amp;
-      cp index.html ${ReportFile} &amp;&amp;
-      mkdir ${ReportFile.files_path} &amp;&amp;
-      cp -r --parents libdir ${ReportFile.files_path} &amp;&amp;
-      cp -r --parents seqclust/clustering/superclusters ${ReportFile.files_path} &amp;&amp;
-      cp -r --parents seqclust/clustering/clusters ${ReportFile.files_path} &amp;&amp;
-      cp seqclust/clustering/hitsort.cls ${ReportFile.files_path}/seqclust/clustering/hitsort.cls &amp;&amp;
-      cp *.png ${ReportFile.files_path}/ &amp;&amp;
-      cp *.csv ${ReportFile.files_path}/ &amp;&amp;
-      cp *.html ${ReportFile.files_path}/  &amp;&amp;
-      cp *.css ${ReportFile.files_path}/  &amp;&amp;
-      cp *.fasta ${ReportFile.files_path}/ 2>>$log  &amp;&amp; rm -r ../tarean_output || :
-
-    </command>
- <inputs>
-	<param name="FastaFile" label="NGS reads" type="data" format="fasta"
-	       help="Input file must contain FASTA-formatted NGS reads. Illumina paired-end reads are recommended."/>
-  <param name="paired" type="boolean" truevalue="--paired" falsevalue="" checked="True" label="Paired-end reads" help="If paired-end reads are used, left- and right-hand reads must be interlaced and all pairs must be complete. Example of the correct format is provided in the help below." />
- 
-  <conditional name="read_sampling">
-    <param name="do_sampling" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Read sampling" help="Use this option if you want to analyze only a part of the reads" />
-    <when value="false">
-      <!-- pass -->
-      <param name="sample" label="Sample size" hidden="True" type="integer" value="0" help="Number of analyzed reads"/>
-    </when>
-    <when value="true">
-      <param name="sample" label="Sample size" type="integer" value="500000" min="10000" help="Number of analyzed reads"/>
-    </when>
-  </conditional>
-
-
-  <param name="taxon" label="Select taxon and protein domain database version (REXdb)" type="select" help="Reference database of transposable element protein domains - REXdb - is used for annotation of repeats">
-    <option value="VIRIDIPLANTAE3.0" selected="true">Viridiplantae version 3.0 </option>
-    <option value="VIRIDIPLANTAE2.2" selected="true">Viridiplantae version 2.2</option>
-    <option value="METAZOA3.0" >Metazoa version 3.0</option>
-    <option value="METAZOA2.0" >Metazoa version 2.0</option>
-    <!-- Modify setting in config.py accordingly -->
-  </param>
-
-  <conditional name="advanced_options">
-    <param name="advanced" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Advanced options" />
-    <when value="false">
-      <!-- pass -->
-    </when>
-    <when value="true">
-      <conditional name="comparative">
-        <param name="options_comparative" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Perform comparative analysis" help="Use this options to analyze multiple samples simultaneously"/>
-	      <when value="false">
-          <!-- do nothing here -->
-        </when>
-        <when value="true">
-   		    <param name="prefix_length" label="Group code length" type="integer" value="3" min="1" max="10" help="For comparative analysis, reads from different samples are distinguished by sample codes included as prefix to the read names. See example below."/>
-        </when>
-      </conditional>
-
-      <conditional name="blastx">
-        <param name="options_blastx" type="select" label="Select parameters for protein domain search">
-          <option value="BLASTX_W2" selected="false">blastx with word size 2 (the most sensitive, slowest)</option>
-          <option value="BLASTX_W3" selected="true">blastx with word size 3 (default)</option>
-          <option value="DIAMOND" selected="false">diamond program (the least sensitive, fastest)</option>
-        </param>
-      </conditional>
-
-      <conditional name="options">
-        <param name="options" type="select" label="Similarity search options">
-          <option value="ILLUMINA" selected="true">Default </option>
-          <option value="ILLUMINA_DUST_OFF" selected="false">Masking of low complexity repeats disabled </option>
-
-          <option value="ILLUMINA_SENSITIVE_MGBLAST" selected="false">Illumina reads, sensitive search (search parameters: mgblast,  min PID 80, -W8) slow, experimental feature!</option>
-          <option value="ILLUMINA_SENSITIVE_BLASTPLUS" selected="false">Illumina reads, more sensitive search (search parameters: blastn,  min PID 80, -W6) extremely slow, experimental feature!</option>
-          <option value="OXFORD_NANOPORE" selected="false">
-            Pseudo short reads simulated from Oxford Nanopore data, experimental feature!
-          </option>
-        </param>
-      </conditional>
-      
-      <conditional name="custom_library">
-	      <param name="options_custom_library" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Use custom repeat database"/>
-	      <when value="false">
-          <!-- do nothing here -->
-        </when>
-        <when value="true">
-   		    <param name="library" format="fasta" type="data" label="Custom repeat database" help="The database should contain DNA sequences in FASTA format. The required format for sequence IDs is : '>reapeatname#class/subclass'"/>
-        </when>
-      </conditional>
-	    <param name="size_threshold" label="Cluster size threshold  for detailed analysis" type="float" value="0.01" min="0.0001" max="100" help ="Minimal size (as percentage of input reads) of the smallest cluster which is analyzed; clusters with less than 20 reads are not considered."/>
-      <param name="automatic_filtering" label="Perform automatic filtering of abundant satellite repeats" help="Automatic filtering identifies the most abundant tandem repeats and partially removes their reads from the analysis. This enables to analyze higher proportions of other less abundant repeats." type="boolean" truevalue="--automatic_filtering" falsevalue="" checked="false"/>
-      <param name="keep_names" label="Keep original read names" type="boolean" truevalue="--keep_names" falsevalue="" checked="false" help="By default, reads are renamed using integers. Use this option to keep original names."/>
-      <param name="assembly_min_cluster_size" type="integer" label="Minimal cluster size for assembly" value="5" min="2" max="100"/>
-    </when>
-  </conditional>
-
-  
-
- </inputs>
-    <outputs>
-	<data name="log" format="txt" label="RepeatExplorer2 - log file"/> 
-	<data name="ReportArchive" format="zip" label="RepeatExplorer2 - Archive with HTML report from data ${FastaFile.hid}"/> 
-	<data name="ReportFile" format="html" label="RepeatExplorer2 - HTML report from data ${FastaFile.hid}"/> 
-    </outputs>
-
-    <help>
-      **HELP**
-      
-      RepeatExplorer2 clustering is a computational pipeline for unsupervised
-      identification of repeats from unassembled sequence reads. The
-      pipeline uses low-pass whole genome sequence reads and performs graph-based
-      clustering. Resulting clusters, representing all types of repeats, are then
-      examined to identify and classify into repeats groups. 
-
-      **Input data**
-      
-      The analysis requires either **single** or **paired-end reads** generated
-      by whole genome shotgun sequencing provided as a single fasta-formatted file.
-      Generally, paired-end reads provide significantly better results than single
-      reads. Reads should be of uniform length (optimal size range is 100-200 nt) and
-      the number of analyzed reads should represent less than 1x genome equivalent
-      (genome coverage of 0.01 - 0.50 x is recommended). Reads should be
-      quality-filtered (recommended filtering : quality score >=10 over 95% of bases
-      and no Ns allowed) and only **complete read pairs** should be submitted for
-      analysis. When paired reads are used, input data must be **interlaced** format
-      as fasta file:
-
-      example of interlaced input format::
-      
-        >0001_f
-        CGTAATATACATACTTGCTAGCTAGTTGGATGCATCCAACTTGCAAGCTAGTTTGATG
-        >0001_r
-        GATTTGACGGACACACTAACTAGCTAGTTGCATCTAAGCGGGCACACTAACTAACTAT
-        >0002_f
-        ACTCATTTGGACTTAACTTTGATAATAAAAACTTAAAAAGGTTTCTGCACATGAATCG
-        >0002_r
-        TATGTTGAAAAATTGAATTTCGGGACGAAACAGCGTCTATCGTCACGACATAGTGCTC
-        >0003_f
-        TGACATTTGTGAACGTTAATGTTCAACAAATCTTTCCAATGTCTTTTTATCTTATCAT
-        >0003_r
-        TATTGAAATACTGGACACAAATTGGAAATGAAACCTTGTGAGTTATTCAATTTATGTT
-        ...
-
-
-      **Comparative analysis**
-
-      For comparative analysis sequence names must contain code (prefix) for each group.
-      Prefix in sequences names  must be of fixed length.
-
-      Example of labeling two groups with where **group code length** is 2 and is used to distinguish groups - AA and BB ::
-
-        >AA0001_f
-        CGTAATATACATACTTGCTAGCTAGTTGGATGCATCCAACTTGCAAGCTAGTTTGATG
-        >AA0001_r
-        GATTTGACGGACACACTAACTAGCTAGTTGCATCTAAGCGGGCACACTAACTAACTAT
-        >AA0002_f
-        ACTCATTTGGACTTAACTTTGATAATAAAAACTTAAAAAGGTTTCTGCACATGAATCG
-        >AA0002_r
-        TATGTTGAAAAATTGAATTTCGGGACGAAACAGCGTCTATCGTCACGACATAGTGCTC
-        >BB0001_f
-        TGACATTTGTGAACGTTAATGTTCAACAAATCTTTCCAATGTCTTTTTATCTTATCAT
-        >BB0001_r
-        TATTGAAATACTGGACACAAATTGGAAATGAAACCTTGTGAGTTATTCAATTTATGTT
-        >BB0002_f
-        TGACATTTGTGAACGTTAATGTTCAACAAATCTTTCCAATGTCTTTTTATCTTATCAT
-        >BB0002_r
-        TATTGAAATACTGGACACAAATTGGAAATGAAACCTTGTGAGTTATTCAATTTATGTT
-        
-
-      To prepare quality filtered and interlaced input fasta file from fastq
-      files, use `Preprocessing of paired-reads`__  tool.
-
-      .. __: tool_runner?tool_id=paired_fastq_filtering
-
-
-      **Additional parameters**
-
-      **Sample size** defines how many reads should be used in calculation.
-      Default setting with 500,000 reads will enable detection of high copy
-      repeats within several hours of computation time. For higher
-      sensitivity the sample size can be set higher. Since sample size affects
-      the memory usage, this parameter may be automatically adjusted to lower
-      value during the run. Maximum sample size which can be processed depends on
-      the repetitiveness of analyzed genome.
-
-      
-      **Select taxon and protein domain database version (REXdb)**. Classification
-      of transposable elements is based on the similarity to our reference database
-      of transposable element protein domains (**REXdb**). Standalone database for Viridiplantae species
-      can be obtained on `repeatexplorer.org`__. Classification
-      system used in REXdb is described in article `Systematic survey of plant
-      LTR-retrotransposons elucidates phylogenetic relationships of their
-      polyprotein domains and provides a reference for element classification`__
-      Database for Metazoa species is still under development so use it with caution.
-
-      .. __: http://repeatexplorer.org
-      .. __: https://doi.org/10.1186/s13100-018-0144-1
-
-      **Select parameters for protein domain search** REXdb is compared with s
-      equence clusters either using blastx or diamond aligner. Diamond program
-      is about three time faster than blastx with word size 3.
-
-      **Similarity search options** By default sequence reads are compared using
-      mgblast program. Default threshold is explicitly set to 90% sequence
-      similarity spanning at least 55% of the read length (in the case of reads
-      differing in length it applies to the longer one). Additionally, sequence
-      overlap must be at least 55 nt. If you select option for shorter reads
-      than 100 nt,  minimum overlap 55 nt is not required.
-
-      By default,
-      mgblast search use DUST program to filter out
-      low-complexity sequences. If you want
-      to increase sensitivity of detection of satellites with shorter monomer
-      use option with '*no masking of low complexity repeats*'. Note that omitting
-      DUST filtering will significantly increase running times
-     
-
-      **Automatic filtering of abundant satellite repeats** perform clustering on
-      smaller dataset of sequence reads to detect abundant high confidence
-      satellite repeats. If such satellites are detected, sequence reads derived
-      from these satellites are depleted from input dataset. This step enable more
-      sensitive detection of less abundant repeats as more reads can be used
-      in clustering step.
-
-      **Use custom repeat database**. This option allows users to perform similarity
-      comparison of identified repeats to their custom databases. The repeat class must
-      be encoded in FASTA headers of database entries in order to allow correct 
-      parsing of similarity hits. Required format for custom database sequence name is: ::
-
-        >reapeatname#class/subclass
-
-
-      **Output**
-
-      List of clusters identified as putative satellite repeats, their genomic
-      abundance and various cluster characteristics. 
-
-      Output includes a **HTML summary** with table listing of all analyzed
-      clusters. More detailed information about clusters is provided in
-      additional files and directories. All results are also provided as
-      downloadable **zip archive**. Additionally a **log file** reporting
-      the progress of the computational pipeline is provided.
-      
-    </help>
-
-</tool>
--- a/repex_tarean.xml	Thu Apr 30 07:42:45 2020 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,251 +0,0 @@
-<tool id="tarean" name="Tandem Repeat Analyzer"  version="2.3.8" >
-    <stdio>
-      <regex match="Traceback" source="stderr" level="fatal" description="Unknown error" />
-      <regex match="error" source="stderr" level="fatal" description="Unknown error" />
-      <regex match="warning" source="stderr" level="warning" description="Unknown warning" />
-      <exit_code range="1:" level="fatal" description="Error" />
-    </stdio>
-    <description>Identification of genomic tandem repeats from NGS data</description>
-    <requirements>
-      <requirement type="package">imagemagick</requirement>
-      <requirement type="package">mafft</requirement>
-      <requirement type="package">blast</requirement>
-      <requirement type="package" version="0.9.29">diamond</requirement>
-      <requirement type="package">blast-legacy</requirement>
-      <requirement type="package">r-igraph</requirement>
-      <requirement type="package">r-data.tree</requirement>
-      <requirement type="package">r-stringr</requirement>
-      <requirement type="package">r-r2html</requirement>
-      <requirement type="package">r-hwriter</requirement>
-      <requirement type="package">r-dt</requirement>
-      <requirement type="package">r-scales</requirement>
-      <requirement type="package">r-plotrix</requirement>
-      <requirement type="package">r-png</requirement>
-      <requirement type="package">r-plyr</requirement>
-      <requirement type="package">r-dplyr</requirement>
-      <requirement type="package">r-optparse</requirement>
-      <requirement type="package">r-dbi</requirement>
-      <requirement type="package">r-rsqlite</requirement>
-      <requirement type="package">r-rserve</requirement>
-      <requirement type="package">bioconductor-biostrings</requirement>
-      <requirement type="package" version="2.3.8">repex_tarean_testing</requirement>
-      <requirement type="set_environment">REPEX</requirement>
-      <requirement type="set_environment">REPEX_VERSION</requirement>
-      <requirement type="package" version="0.9.1">pyrserve</requirement>
-    </requirements>
-  <command detect_errors="exit_code">
-    export PYTHONHASHSEED=0;
-    \${REPEX}/seqclust --paired --sample ${read_sampling.sample} --output_dir=tarean_output --logfile=${log} --cleanup --tarean_mode
-    #if $advanced_options.advanced:
-      --mincl $advanced_options.size_threshold $advanced_options.keep_names $advanced_options.automatic_filtering -M $advanced_options.merging
-      #if $advanced_options.custom_library.options_custom_library :
-     	  -d $advanced_options.custom_library.library extra_database
-      #end if
-      #if $advanced_options.options.options:
-        -opt $advanced_options.options.options
-      #end if   
-    #else:
-      -M 0.2
-
-    #end if
-    ${FastaFile} >stdout.log 2> stderr.log ;
-    echo "STDOUT CONTENT:" >> ${log} ;
-    cat stdout.log >> ${log} ;
-    echo "STDERR CONTENT:" >> ${log} ;
-    cat stderr.log >> ${log} &amp;&amp;
-    \${REPEX}/stderr_filter.py stderr.log &amp;&amp;
-    cd tarean_output &amp;&amp;
-    zip -r  ${ReportArchive}.zip * &amp;&amp;
-    mv ${ReportArchive}.zip ${ReportArchive} &amp;&amp;
-    cp index.html ${ReportFile} &amp;&amp;
-    mkdir ${ReportFile.files_path} &amp;&amp;
-    cp -r --parents libdir ${ReportFile.files_path} &amp;&amp;
-    cp -r --parents seqclust/clustering/superclusters ${ReportFile.files_path} &amp;&amp;
-    cp -r --parents seqclust/clustering/clusters ${ReportFile.files_path} &amp;&amp;
-    cp seqclust/clustering/hitsort.cls ${ReportFile.files_path}/seqclust/clustering/hitsort.cls &amp;&amp;
-    cp *.png ${ReportFile.files_path}/ &amp;&amp;
-    cp *.csv ${ReportFile.files_path}/ &amp;&amp;
-    cp *.html ${ReportFile.files_path}/  &amp;&amp;
-    cp *.css ${ReportFile.files_path}/  &amp;&amp;
-    cp *.fasta ${ReportFile.files_path}/ 2>>$log  &amp;&amp; rm -r ../tarean_output || :
-
-    
-  </command>
-
-  <inputs>
-	  <param name="FastaFile" label="Paired-end Illumina reads" type="data" format="fasta"
-	         help="Input file must contain FASTA-formatted interlaced read pairs from paired-end sequencing. All pairs must be complete. Example of the input data format is provided in the help below."/>
-
-    <conditional name="read_sampling">
-      <param name="do_sampling" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Read sampling" help="Use this option if you want to analyze only a part of the reads" />
-      <when value="false">
-        <!-- pass -->
-        <param name="sample" label="Sample size" hidden="True" type="integer" value="0" help="Number of analyzed reads"/>
-      </when>
-      <when value="true">
-        <param name="sample" label="Sample size" type="integer" value="500000" min="10000" help="Number of analyzed reads"/>
-      </when>
-    </conditional>
-
-    <conditional name="advanced_options">
-      <param name="advanced" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Advanced options" />
-      <when value="false">
-        <!-- pass -->
-      </when>
-      <when value="true">
-        <param name="merging" type="boolean" truevalue="0.2" falsevalue="0" checked="True" label="Perform cluster merging" help="By default, clusters connected through paired-end reads are merged"/>
-        <conditional name="custom_library">
-	        <param name="options_custom_library" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Use custom repeat database"/>
-	        <when value="false">
-            <!-- do nothing here -->
-          </when>
-          <when value="true">
-	          <param name="library" format="fasta" type="data" label="Use custom repeat database" help="Perform additional similarity search to user-provided repeat database. The database should contain FASTA-formatted DNA sequences with headers (sequence names) in the format: '>reapeatname#class/subclass'"/>
-          </when>
-        </conditional>
-        <param name="size_threshold" label="Cluster size threshold for detailed analysis" type="float" value="0.01" min="0.0001" max="100" help ="Minimal size (as percentage of input reads) of the smallest cluster which is analyzed; cluster with less than 20 reads are not considered."/>
-        <param name="automatic_filtering" label="Perform automatic filtering of abundant satellite repeats" type="boolean" truevalue="--automatic_filtering" falsevalue="" checked="false"/>
-        <param name="keep_names" label="Keep original read names" type="boolean" truevalue="--keep_names" falsevalue="" checked="false" help="By default, reads are renamed using integers. Use this option if you want to keep original names."/>
-        <conditional name="options">
-          <param name="options" type="select" label="Similarity search options">
-            <option value="ILLUMINA" selected="true">Default </option>
-            <option value="ILLUMINA_DUST_OFF" selected="false">Masking of low complexity repeats disabled </option>
-
-            <option value="ILLUMINA_SENSITIVE_MGBLAST" selected="false">Illumina reads, sensitive search (search parameters: mgblast,  min PID 80, -W8) slow, experimental feature!</option>
-          <option value="ILLUMINA_SENSITIVE_BLASTPLUS" selected="false">Illumina reads, more sensitive search (search parameters: blastn,  min PID 80, -W6) extremely slow, experimental feature!</option>
-          <option value="OXFORD_NANOPORE" selected="false">
-            Pseudo short reads simulated from Oxford Nanopore data, experimental feature!
-          </option>
-          </param>
-        </conditional>
-      </when>
-    </conditional>
-
-    
-
-  </inputs>
-  <outputs>
-	  <data name="log" format="txt" label="TAREAN log file"/> 
-	  <data name="ReportArchive" format="zip" label="TAREAN Archive with HTML report from data ${FastaFile.hid}"/> 
-	  <data name="ReportFile" format="html" label="TAREAN HTML report from data ${FastaFile.hid}"/> 
-  </outputs>
-
-  <help>
-    **HELP**
-    
-    TAREAN - TAndem REpeat ANalyzer is a computational pipeline for
-    **unsupervised identification of satellite repeats** from unassembled
-    sequence reads. The pipeline uses low-pass paired-end whole genome
-    sequence reads and performs graph-based clustering. The resulting
-    clusters, representing all types of repeats present in the genome, are
-    then examined to identify those containing circular structures indicative
-    of tandem repeats. A poster summarizing TAREAN principles and
-    implementation can be found `here.`__
-
-
-    .. __: http://w3lamc.umbr.cas.cz/lamc/?page_id=312
-
-    **Input data**
-    
- 
-    The analysis requires **paired-end reads** generated by whole genome
-    shotgun sequencing. The data should be provided as a single input file in
-    fasta format with the reads interlaced (see example below). All the pairs
-    must be complete, i.e. both "forward" and "reverse" sequence reads must be
-    present. The reads should all be trimmed to the same length. The optimal
-    size range is between 100 and 200 nucleotides. The number of reads to be
-    analyzed should not exceed 1x coverage of the genome. Genome coverage
-    between 0.01 and 0.5x is recommended. The reads should be filtered for
-    quality. The recommended quality filtering is as follows: each read should
-    have a quality score >=10 for 95% of the bases, i.e. if your reads are 100
-    base pairs long, then a read only passes this quality threshold if 95
-    bases have a quality of 10 or higher. Additionally, any reads containing
-    indeterminate base pairs (indicated as N in the reads) should be removed.
-    Finally, if either one of the reads in a pair fails to meet the
-    aforementioned thresholds, **both** sequences should be removed.
-    example of interlaced input format::
-    
-      >0001_f
-      CGTAATATACATACTTGCTAGCTAGTTGGATGCATCCAACTTGCAAGCTAGTTTGATG
-      >0001_r
-      GATTTGACGGACACACTAACTAGCTAGTTGCATCTAAGCGGGCACACTAACTAACTAT
-      >0002_f
-      ACTCATTTGGACTTAACTTTGATAATAAAAACTTAAAAAGGTTTCTGCACATGAATCG
-      >0002_r
-      TATGTTGAAAAATTGAATTTCGGGACGAAACAGCGTCTATCGTCACGACATAGTGCTC
-      >0003_f
-      TGACATTTGTGAACGTTAATGTTCAACAAATCTTTCCAATGTCTTTTTATCTTATCAT
-      >0003_r
-      TATTGAAATACTGGACACAAATTGGAAATGAAACCTTGTGAGTTATTCAATTTATGTT
-      ...
-
-
-    To perform the quality filtering on your fastQ formatted data as described
-    above, and to interlace your paired-end sequence reads,
-    please use the `Preprocessing of paired-reads`__  tool.
-
-    .. __: tool_runner?tool_id=paired_fastq_filtering
-
-
-    **Additional parameters**
-
-    **Sample size** defines how many reads will be used during the computation.
-    The default setting of 500,000 reads will enable detection of high copy
-    number satellites within several hours. For higher
-    sensitivity the sample size can be increased. Since the sample size affects
-    memory usage, this parameter may be automatically adjusted to a lower value
-    during the run. The maximum sample size which can be processed depends on the
-    repetitiveness of the analyzed genome. This significantly limits the number of reads
-    that can be analyzed with the TAREAN pipeline.
-
-    **Perform cluster merging**. Families of repetitive elements are
-    frequently split into multiple clusters rather than being represented as a
-    single one. If you do not want to merge clusters based on the presence
-    of broken read pairs, disable this option. 
-    
-    **Use custom repeat database**. This option allows users to perform similarity
-    comparison of identified repeats to their custom databases. The repeat class should
-    be encoded in FASTA headers of database entries in order to allow correct 
-    parsing of similarity hits.
-
-    **Similarity search options** By default sequence reads are compared using
-    mgblast program. Default threshold is explicitly set to 90% sequence
-    similarity spanning at least 55% of the read length (in the case of reads
-    differing in length it applies to the longer one). Additionally, sequence
-    overlap must be at least 55 nt. If you select option for shorter reads
-    than 100 nt,  minimum overlap 55 nt is not required.
-    
-    By default,
-    mgblast search use DUST program to filter out
-    low-complexity sequences. If you want
-    to increase sensitivity of detection of satellites with shorter monomer
-    use option with '*no masking of low complexity repeats*'. Note that omitting
-    DUST filtering will significantly increase running times
-    
-    **Output**
-
-    A list of clusters identified as putative satellite repeats, their genomic
-    abundance and various cluster characteristics are provided. Length and
-    consensus sequences of reconstructed monomers are also shown and
-    accompanied by a detailed output from kmer-based reconstruction including
-    sequences and sequence logos of alternative variants of monomer sequences.
-
-    The output includes an **HTML summary** with a table listing all analyzed
-    clusters. More detailed information about clusters is provided in
-    additional files and directories. All results are also provided as a
-    downloadable **zip archive**. Since read clustering results in
-    thousands of clusters, the search for satellite repeats is limited to
-    a subset of the largest ones corresponding to the most abundant genomic
-    repeats. The default setting of the pipeline is to analyze all clusters containing at least
-    0.01% of the input reads. Besides the satellite repeats, three other
-    groups of clusters are reported in the output (1) LTR-retrotransposons,
-    (2) 45S and 5S rDNA and (3) all remaining clusters passing the size
-    threshold. As (1) and (2) contain sequences with circular
-    graphs, their consensus is calculated in the same way as for satellite
-    repeats. Additionally a **log file** reporting the progress of the
-    computational pipeline is provided.
-
-    
-  </help>
-
-</tool>
--- a/tool_dependencies.xml	Thu Apr 30 07:42:45 2020 -0400
+++ b/tool_dependencies.xml	Fri Jul 24 07:26:07 2020 -0400
@@ -1,9 +1,28 @@
-<?xml version="1.0" ?>
+<?xml version="1.0"?>
 <tool_dependency>
-    <package name="repex_tarean_testing" version="2.3.8">
-        <repository changeset_revision="31743c5c3fc7" name="package_repex_tarean_testing_2_3_8" owner="petr-novak" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu"/>
-        <readme>
-      prepare repex database and scripts
+  <package name="repex_tarean_dev" version="2.3.8">
+    <install version="1.0">
+      <actions>
+        <action type="download_by_url">https://bitbucket.org/petrnovak/repex_tarean/get/7fa000f91080.zip</action>
+        <action type="shell_command">
+          make
+        </action>
+        <action type="move_directory_files">
+          <source_directory>$TMP_WORK_DIR/petrnovak-repex_tarean-7fa000f91080</source_directory>
+          <destination_directory>$INSTALL_DIR</destination_directory>
+        </action>
+
+        <action type="set_environment">
+          <environment_variable action="set_to" name="REPEX">$INSTALL_DIR</environment_variable>
+        </action>
+        <action type="set_environment">
+          <environment_variable action="set_to" name="REPEX_VERSION">"version: 0.3.8-458(7fa000f) branch: almitey"</environment_variable>
+        </action>
+      </actions>
+    </install>
+    <readme>
+      repeatexplorer executables and databases
     </readme>
-    </package>
-</tool_dependency>
\ No newline at end of file
+  </package>
+</tool_dependency>
+