# HG changeset patch
# User Eric Badger <badger@msi.umn.edu>
# Date 1396980966 18000
# Node ID 961b5bf3fcc85339a837ad6623b163518df711b4
# Parent  6425d1da3746552aba49ecb72164776875bf48e2
remove other tools

diff -r 6425d1da3746 -r 961b5bf3fcc8 RSEM_abundance_estimation.xml
--- a/RSEM_abundance_estimation.xml	Fri Apr 04 15:30:44 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,91 +0,0 @@
-<tool id="RSEM_abundance_estimation" name="RSEM abundance estimation" version="0.0.2">
-    <description>run RSEM to estimate transcript abundances</description>
-    <requirements>
-        <requirement type="package" version="2013_08_14">trinityrnaseq</requirement>
-        <requirement type="package" version="1.1.17">rsem</requirement>
-    </requirements>
-    <command>
-        \$TRINITY_HOME/util/RSEM_util/run_RSEM_align_n_estimate.pl  --transcripts $transcripts 
-        ## Inputs.
-        #if str($read_type.paired_or_single) == "single":
-            #if  $read_type.single_reads.extension.startswith( "fastq"):
-                --seqType fq
-            #else
-                --seqType fa
-            #end if
-            --single $read_type.single_reads
-        #else
-            #if  $read_type.left_reads.extension.startswith( "fastq"):
-                --seqType fq
-            #else
-                --seqType fa
-            #end if
-            --left $read_type.left_reads
-            --right $read_type.right_reads
-        #end if
-        #if $transcript.source == "other":
-            --no_group_by_component
-            --gene_trans_map $transcript.gene_trans_map
-        #end if         
-    </command>
-    <inputs>
-        <param name="transcripts" type="data" format="fasta" label="transcripts_fasta" help="Fasta sequences for which reads are aligned."  />
-        <conditional name="read_type">
-            <param name="paired_or_single" type="select" label="Paired or Single-end data?">
-                <option value="paired">Paired</option>
-                <option value="single">Single</option>
-            </param>
-            <when value="paired">
-                <param name="left_reads" type="data" format="fasta,fastq" label="left reads" help=""  />
-                <param name="right_reads" type="data" format="fasta,fastq" label="right reads" help=""  />
-                <param name="ss_lib_type" type="select" label="strand-specific library type">
-                    <option value="RF">RF</option>
-                    <option value="FR">FR</option>
-                </param>
-            </when>
-            <when value="single">
-                <param name="single_reads" type="data" format="fasta,fastq" label="single reads" help=""  />
-                <param name="ss_lib_type" type="select" label="strand-specific library type">
-                    <option value="F">F</option>
-                    <option value="R">R</option>
-                </param>
-            </when>
-        </conditional>
-        <conditional name="transcript">
-            <param name="source" type="select" label="Transcripts Source">
-                <option value="trinity">Trinity</option>
-                <option value="other">NOT trinity</option>
-            </param>
-            <when value="trinity"/>
-            <when value="other">
-                <param name="gene_trans_map" type="data" format="tabular" optional="true" label="Map of gene ids to transcript (isoform) ids" >
-                  <help>
-                    Each line of should be of the form: gene_id transcript_id ( with the two fields separated by a tab character )
-                  </help>
-                </param>
-            </when>
-        </conditional>
-    </inputs>
-    <stdio>
-        <exit_code range="1:"  level="fatal" description="Error Running RSEM" />
-    </stdio>
-    <outputs>
-        <data format="text" name="transcript_counts" label="${tool.name} on ${on_string}: Isoform Counts" from_work_dir="RSEM.isoforms.results"/>
-        <data format="text" name="gene_counts" label="${tool.name} on ${on_string}: Gene counts" from_work_dir="RSEM.genes.results"/>
-    </outputs>
-    <tests>
-        <test>
-            <param name="target" value="trinity/Trinity.fasta" />
-            <param name="aligner" value="bowtie" />
-            <param name="paired_or_single" value="single" />
-            <param name="library_type" value="None" />
-            <param name="input" value="trinity/reads.left.fq" />
-        </test>
-    </tests>
-    <help>
-        .. _Trinity: http://trinityrnaseq.sourceforge.net
-
-        $TRINITY_HOME/util/RSEM_util/run_RSEM_align_n_estimate.pl --transcripts Trinity.fasta \
-        --seqType fq --left left.reads.fq --right right.reads.fq
-    </help>
-</tool>
diff -r 6425d1da3746 -r 961b5bf3fcc8 tool_dependencies.xml
--- a/tool_dependencies.xml	Fri Apr 04 15:30:44 2014 -0500
+++ b/tool_dependencies.xml	Tue Apr 08 13:16:06 2014 -0500
@@ -9,11 +9,5 @@
     <package name="bowtie" version="1.0.0">
         <repository changeset_revision="e682af6a72cd" name="package_bowtie_1_0_0" owner="jjohnson" toolshed="http://testtoolshed.g2.bx.psu.edu" />
     </package>
-    <package name="hmmer" version="3.0">
-        <repository changeset_revision="a44693e3a2c4" name="package_hmmer_3_0" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="rsem" version="1.1.17">
-        <repository changeset_revision="7d060ea51c6f" name="package_rsem_1_1_17" owner="jjohnson" toolshed="http://testtoolshed.g2.bx.psu.edu" />
-    </package>
 </tool_dependency>
 
diff -r 6425d1da3746 -r 961b5bf3fcc8 transcriptsToOrfs.xml
--- a/transcriptsToOrfs.xml	Fri Apr 04 15:30:44 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,117 +0,0 @@
-<tool id="transcriptsToOrfs" name="transcriptsToOrfs" version="0.0.2">
-    <description>Trinity Transcripts to Candidate Peptides</description>
-    <requirements>
-        <requirement type="package" version="2013_08_14">trinityrnaseq</requirement>
-        <requirement type="package" version="3.0">hmmer</requirement>
-    </requirements>
-    <command>
-        \$TRINITY_HOME/trinity-plugins/transdecoder/transcripts_to_best_scoring_ORFs.pl
-        -t $transcripts 
-        #if $min_prot_length:
-            -m $min_prot_length 
-        #end if 
-        #if $retain_long_orfs:
-            --retain_long_orfs $retain_long_orfs 
-        #end if 
-        #if $training_count:
-            -T $training_count 
-        #end if 
-        #if str($strand_specificity) == 'SS':
-            -S
-        #end if
-        #if $genetic_code.__str__ != '':
-            -G $genetic_code
-        #end if
-        #if $search.use_pfam == 'yes':
-          --search_pfam "${ filter( lambda x: str( x[0] ) == str( $search.pfam_db ), $__app__.tool_data_tables[ 'pfam_databases' ].get_fields() )[0][-1] }"
-          --CPU $search.CPU
-        #end if
-    </command>
-    <inputs>
-        <param format="fasta" name="transcripts" type="data" label="Transcripts sequences in fastA format" help="" />
-        <param name="min_prot_length"  type="integer" value="" optional="true" label="Minimum peptide length (in amino acids)" help="default: 100">
-            <validator type="in_range" message="Minimum peptide length should be at least 50" min="50" />
-        </param>
-        <param name="retain_long_orfs"  type="integer" value="" optional="true" label="Retain all ORFs found that are of minimum length in nucleotides" help="default: 900" >
-            <validator type="in_range" message="ORF length should be at least 50" min="50" />
-        </param>
-        <param name="training_count"  type="integer" value="" optional="true" label="Number of top longest ORFs to train Markov Model (hexamer stats)" help="default: 500" >
-            <validator type="in_range" message="ORF count should be at least 50" min="50" />
-        </param>
-        <param name="strand_specificity" type="select" label="Strand specificity type">
-            <option value="DS">NOT strand specific, examine both strands</option>
-            <option value="SS">Strand specific, examine only top strand</option>
-        </param>
-        <param name="genetic_code" type="select" label="Genetic Code">
-            <option value="">use default(universal)</option>
-            <option value="universal">universal</option>
-            <option value="Euplotes">Euplotes</option>
-            <option value="Tetrahymena">Tetrahymena</option>
-            <option value="Candida">Candida</option>
-            <option value="Acetabularia">Acetabularia</option>
-        </param>
-        <conditional name="search">
-            <param name="use_pfam" type="select" label="Search PFAM database">
-                <option value="no">NO</option>
-                <option value="yes">YES</option>
-            </param>
-            <when value="no"/>
-            <when value="yes">
-                <param name="pfam_db" type="select" label="Pfam database">
-                    <options from_data_table="pfam_databases" />
-                </param>
-                <param name="CPU" type="integer" value="2" min="1" label="CPU" help="Number of CPUs to use by hmmscan" />
-            </when>
-        </conditional>
-    </inputs>
-    <stdio>
-        <exit_code range="1:"  level="fatal" description="Failed" />
-        <regex match="Error" 
-               source="stderr" 
-               level="fatal" 
-               description="Failed" />
-    </stdio>
-    <outputs>
-        <data format="txt" name="trinity_pep_pfam" label="${tool.name} on ${on_string}: Pfam matches to Candidate Peptide Sequences" from_work_dir="longest_orfs.pep.pfam.dat">
-          <filter>search['use_pfam'] == 'yes'</filter>
-        </data>
-        <data format="gff3" name="trinity_pep_gff3" label="${tool.name} on ${on_string} Candidate Peptide Features" from_work_dir="best_candidates.eclipsed_orfs_removed.gff3" />
-        <data format="bed" name="trinity_pep_bed" label="${tool.name} on ${on_string} Candidate Peptide Coordinates" from_work_dir="best_candidates.eclipsed_orfs_removed.bed" />
-        <data format="fasta" name="trinity_pep_cds" label="${tool.name} on ${on_string}: Candidate Peptide CDS Sequences" from_work_dir="best_candidates.eclipsed_orfs_removed.cds"/>
-        <data format="fasta" name="trinity_pep_seqs" label="${tool.name} on ${on_string}: Candidate Peptide Sequences" from_work_dir="best_candidates.eclipsed_orfs_removed.pep"/>
-    </outputs>
-    <tests>
-        <test>
-            <param name="transcripts" ftype="fasta" value="TrinitySingle.fasta"/>
-            <param name="min_prot_length" value="100"/>
-            <param name="use_pfam" value="no"/>
-            <output name="trinity_pep_seqs">
-                <assert_contents>
-                    <has_text text="WAAKAWLITARSLYPADF" />
-                </assert_contents>
-            </output>
-            <output name="trinity_pep_cds">
-                <assert_contents>
-                    <has_text text="TGGGCAGCCAAGGCATGGCTGATCACGGCCCGCA" />
-                </assert_contents>
-            </output>
-            <output name="trinity_pep_bed">
-                <assert_contents>
-                    <has_text text="comp10_c0_seq1" />
-                </assert_contents>
-            </output>
-            <output name="trinity_pep_gff3">
-                <assert_contents>
-                    <has_text text="comp10_c0_seq1" />
-                </assert_contents>
-            </output>
-        </test>
-    </tests>
-    <help>
-        ** transcriptsToOrfs ** 
-        Trinity_ is a de novo transcript assembler that uses RNA-seq data as input. 
-        This tool searches for open reading frames in the assembled transcripts.
-        
-        .. _Trinity: http://trinityrnaseq.sourceforge.net
-    </help>
-</tool>
diff -r 6425d1da3746 -r 961b5bf3fcc8 trinityrnaseq.xml
--- a/trinityrnaseq.xml	Fri Apr 04 15:30:44 2014 -0500
+++ b/trinityrnaseq.xml	Tue Apr 08 13:16:06 2014 -0500
@@ -1,4 +1,4 @@
-<tool id="trinityrnaseq" name="Trinity" version="0.0.3">
+<tool id="trinityrnaseq-itasca" name="Trinity - Itasca BETA" version="0.0.3">
     <!-- Written by Jeremy Goecks, now maintained here by bhaas -->
     <description>De novo assembly of RNA-Seq data Using Trinity</description>
     <requirements>
@@ -51,10 +51,10 @@
     </command>
     <inputs>
       <param name="computenode" type="select" label="Compute node" help="Select the size of node needed">
-        <option value="22G">22GB - 8 cores</option>
-        <option value="62G">62GB - 16 cores</option>
-        <option value="126G">126GB - 16 cores</option>
-        <option value="256G">254GB - 16 cores</option>
+        <option value="21G">21GB - 8 cores</option>
+        <option value="58G">58GB - 16 cores</option>
+        <option value="125G">125GB - 16 cores</option>
+        <option value="253G">253GB - 16 cores</option>
       </param>
 
         <conditional name="inputs">
diff -r 6425d1da3746 -r 961b5bf3fcc8 trinityrnaseq_norm.xml
--- a/trinityrnaseq_norm.xml	Fri Apr 04 15:30:44 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,178 +0,0 @@
-<tool id="trinityrnaseq_norm" name="Trinity read normalization" version="0.0.2">
-    <!-- Written by Jeremy Goecks, modified by Josh Bowden for normalization proceedure, now maintained here by bhaas -->
-    <description>Pre-process RNA-seq data to reduce coverage of highly covered areas</description>
-    <requirements>
-        <requirement type="package" version="2013_08_14">trinityrnaseq</requirement>
-    </requirements>
-    <command>
-        ## symlink input in work_dir
-        #if str($inputs.paired_or_single) == "paired":
-          ln -s $inputs.left_input left_reads &amp;&amp;
-          ln -s $inputs.right_input right_reads &amp;&amp;
-        #else:
-          ln -s $inputs.input single_reads &amp;&amp;
-        #end if	
-        \${TRINITY_HOME}/util/normalize_by_kmer_coverage.pl --JM $JM --max_cov $max_cov
-        ## Inputs.
-        #if str($inputs.paired_or_single) == "paired":
-            --left left_reads --right right_reads
-            #if  $inputs.left_input.ext == 'fa':
-                --seqType fa
-            #else:
-                --seqType fq
-            #end if
-            $inputs.pe_reads_unordered
-            #if str($inputs.library_type) != "None":
-                --SS_lib_type $inputs.library_type
-            #end if
-            $inputs.pairs_together
-            $inputs.parallel_stats
-        #else:
-            --single single_reads
-            #if  str($inputs.input.ext) == 'fa':
-                --seqType fa
-            #else:
-                --seqType fq
-            #end if
-            #if str($inputs.library_type) != "None":
-                --SS_lib_type $inputs.library_type
-            #end if
-        #end if	
-        #if $kmer_size:
-            --KMER_SIZE $kmer_size
-        #end if
-        #if $max_pct_stdev:
-            --max_pct_stdev $max_pct_stdev
-        #end if
-        ## direct stdio to output
-        | tee  $trinity_coverage_normalization_log &amp;&amp;
-        #if str($inputs.paired_or_single) == "paired":
-          cp left_reads.normalized* $output_left &amp;&amp;
-          cp right_reads.normalized* $output_right 
-        #else:
-          cp single_reads.normalized* $output_single 
-        #end if	
-    </command>
-    <inputs>
-      	<param name="JM" type="select" label="JM" help="Amount of memory to allocate to Jellyfish for Kmer catalog construction">
-		<option value="1G">1G</option>
-		<option value="10G">10G</option>
-		<option value="20G">20G</option>
-		<option value="50G">50G</option>
-		<option value="100G">100G</option>			
-	</param>
-		
-	<param name="max_cov" type="select" label="max_cov" help="Read coverage in terms of maximum covarge to keep">
-		<option value="30">30</option>
-		<option value="40">40</option>
-		<option value="50">50</option>
-		<option value="60">60</option>
-		<option value="70">70</option>
-		<option value="100">100</option>
-	</param>
-
-        <conditional name="inputs">
-	    <param name="paired_or_single" type="select" label="Paired or Single-end data?">
-                <option value="paired">Paired</option>
-                <option value="single">Single</option>
-            </param>
-            <when value="paired">
-                <param format="fasta,fastq" name="left_input" type="data" label="Left/Forward strand reads" help=""/>
-                <param format="fasta,fastq" name="right_input" type="data" label="Right/Reverse strand reads" help=""/>
-                <param name="library_type" type="select" label="Strand-specific Library Type">
-                    <option value="None">None</option>
-                    <option value="FR">FR</option>
-                    <option value="RF">RF</option>
-                </param>  				
-                <param name="pe_reads_unordered" type="boolean" truevalue="--PE_reads_unordered" falsevalue="" checked="false" label="set if the input paired-end reads are not identically ordered"/>
-                <param name="pairs_together" type="boolean" truevalue="--pairs_together" falsevalue="" checked="false" label="process paired reads by averaging stats between pairs and retaining linking info"/>
-                <param name="parallel_stats" type="boolean" truevalue="--PARALLEL_STATS" falsevalue="" checked="false" label="generate read stats in parallel for paired reads" help="(Figure 2X Inchworm memory requirement)"/>
-            </when>
-            <when value="single">
-                <param format="fasta,fastq" name="input" type="data" label="Single-end reads" help=""/>
-                <param name="library_type" type="select" label="Strand-specific Library Type">
-                    <option value="None">None</option>
-                    <option value="F">F</option>
-                    <option value="R">R</option>
-                </param>
-            </when>
-        </conditional>
-        <param name="kmer_size"  type="integer" value="" optional="true" label="KMER SIZE" help="default: 25">
-            <validator type="in_range" message="kmer size between 3 and 200" min="3" max="200"/>
-        </param>
-        <param name="max_pct_stdev"  type="integer" value="" optional="true" label="maximum pct of mean for stdev of kmer coverage across read" help="default: 100">
-            <validator type="in_range" message="kmer size between 10 and 100" min="10" max="100"/>
-        </param>
-        
-    </inputs>
-    <stdio>
-        <exit_code range="1:"  level="fatal" description="Failed" />
-        <regex match="Error" 
-               source="stdout" 
-               level="fatal" 
-               description="Failed" />
-    </stdio>
-    <outputs>
-	<!-- I have not found a way to do condional outputs so all potential output files are specified and some will be empty -->
-	<data format="txt" name="trinity_coverage_normalization_log" label="${tool.name} on ${on_string}: log" />
-	<data format_source="left_input" name="output_left" label="${tool.name} on ${on_string}: Normalized left reads"> 
-            <filter>inputs['paired_or_single'] == "paired"</filter>
-        </data>
-	<data format_source="right_input" name="output_right" label="${tool.name} on ${on_string}: Normalized right reads"> 
-            <filter>inputs['paired_or_single'] == "paired"</filter>
-        </data>
-	<data format_source="input" name="output_single" label="${tool.name} on ${on_string}: Normalized reads"> 
-            <filter>inputs['paired_or_single'] == "single"</filter>
-        </data>
-    </outputs>
-    <tests>
-        <test>
-            <param name="JM" value="1G"/>
-            <param name="max_cov" value="30"/>
-            <param name="paired_or_single" value="single"/>
-            <param name="input" ftype="fastq" value="reads.left.fq"/>
-            <param name="library_type" value="None"/>
-            <output name="trinity_coverage_normalization_log">
-                <assert_contents>
-                    <has_text text="Normalization complete." />
-                </assert_contents>
-            </output>
-            <output name="output_single">
-                <assert_contents>
-                    <has_text text="ACTGCATCCTGGAAAGAATCAATGGTGGCCGGAAAGTGTTTTTCAAATACAAGAGTGACAATGTGCCCTGTTGTTT" />
-                </assert_contents>
-            </output>
-        </test>
-        <test>
-            <param name="JM" value="1G"/>
-            <param name="max_cov" value="30"/>
-            <param name="paired_or_single" value="paired"/>
-            <param name="left_input" ftype="fastq" value="reads.left.fq"/>
-            <param name="right_input" ftype="fastq" value="reads.right.fq"/>
-            <param name="library_type" value="None"/>
-            <param name="pe_reads_unordered" value="False"/>
-            <param name="pairs_together" value="False"/>
-            <param name="parallel_stats" value="False"/>
-            <output name="trinity_coverage_normalization_log">
-                <assert_contents>
-                    <has_text text="Normalization complete." />
-                </assert_contents>
-            </output>
-            <output name="output_left">
-                <assert_contents>
-                    <has_text text="CTGGGCTGCAGCTAAGTTCTCTGCATCCTCCTTCTTGCTTGTGGCTGGGAAGAAGACAATGTTGTCGATGGTCTGG" />
-                </assert_contents>
-            </output>
-            <output name="output_right">
-                <assert_contents>
-                    <has_text text="CTCAAATGGTTAATTCTCAGGCTGCAAATATTCGTTCAGGATGGAAGAACATTTTCTCAGTATTCCATCTAGCTGC" />
-                </assert_contents>
-            </output>
-        </test>
-    </tests>
-    <help>
-        Runs script Trinity_ script util/normalize_by_kmer_coverage.pl which reduces data sizes with minimal impact on recovered transcripts when used by Trinity.pl.
-        
-        .. _Trinity: http://trinityrnaseq.sourceforge.net
-    </help>
-</tool>