# HG changeset patch
# User bgruening
# Date 1535054306 14400
# Node ID 6b0ba6de14249b47143a5ed043f5086dcd7e6912
# Parent  e7e885f718fb8f5e6b7f73fb161a3b217f04f52e
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56

diff -r e7e885f718fb -r 6b0ba6de1424 README.rst
--- a/README.rst	Wed May 30 03:19:09 2018 -0400
+++ b/README.rst	Thu Aug 23 15:58:26 2018 -0400
@@ -1,10 +1,10 @@
 Galaxy wrappers for salmon
 =====================================
 
-These wrappers are copyright 2014, updated 2016 by Björn Grüning, Mhd Ramez Alrawas and additional contributors.
+These wrappers are copyright 2014, updated 2018 by Björn Grüning, Mhd Ramez Alrawas and additional contributors.
 All rights reserved. See the licence text below.
 
-Currently tested with salmon 0.7.2.
+Currently tested with salmon 0.11.2.
 
 
 Automated Installation
@@ -23,6 +23,12 @@
 v0.6.3.0  - First release
 -------- ----------------------------------------------------------------------
 v0.7.2    - Second release
+-------- ----------------------------------------------------------------------
+v0.8.2    - Third release
+-------- ----------------------------------------------------------------------
+v0.9.1    - Fourth release
+-------- ----------------------------------------------------------------------
+v0.11.2   - Fifth release
 
 ======== ======================================================================
 
diff -r e7e885f718fb -r 6b0ba6de1424 salmon.xml
--- a/salmon.xml	Wed May 30 03:19:09 2018 -0400
+++ b/salmon.xml	Thu Aug 23 15:58:26 2018 -0400
@@ -17,7 +17,7 @@
                 <option value="I" selected="True">Mates are oriented toward each other (I = inward)</option>
             </param>
         </xml>
-        <token name="@VERSION@">0.9.1</token>
+        <token name="@VERSION@">0.11.2</token>
     </macros>
 
     <requirements>
@@ -47,9 +47,6 @@
                 --index './index'
                 --type '$quasi_orphans.type'
                 $perfectHash
-                #if str($sasamp):
-                    --sasamp $sasamp
-                #end if
             #set $index_path = './index'
         #else:
             #set $index_path = $refTranscriptSource.index.fields.path
@@ -122,6 +119,7 @@
                     --unmatedReads ./single.$ext
                 #end if
             #else:
+                --libType "${single_or_paired.orientation}${single_or_paired.strandedness}"
                 #if $single_or_paired.single_or_paired_opts == 'paired_interleaved':
                     #if $compressed == 'BZ2':
                         --mates1 <(bzcat < ./mate1.$ext | seqtk seq -1)
@@ -142,16 +140,20 @@
                         --mates2 ./mate2.$ext
                     #end if
                 #end if
-                --libType "${single_or_paired.orientation}${single_or_paired.strandedness}"
             #end if
             --output ./output
             #if str($quasi_orphans.type) == 'quasi':
                 --allowOrphans
-            #else:
-                $quasi_orphans.allowOrphans
+                $quasi_orphans.validateMappings
+                --ma $quasi_orphans.matchScore
+                --mp $quasi_orphans.mismatchPenalty
+                --go $quasi_orphans.gapOpenPenalty
+                --ge $quasi_orphans.gapExtensionPenalty
+                --minScoreFraction $quasi_orphans.minScoreFraction
             #end if
             $seqBias
             $gcBias
+            $noErrorModel
             --threads "\${GALAXY_SLOTS:-4}"
             --incompatPrior $adv.incompatPrior
             $adv.consistentHits
@@ -173,9 +175,6 @@
             #if $adv.forgettingFactor:
                 --forgettingFactor $adv.forgettingFactor
             #end if
-            #if str($adv.maxOcc):
-                --maxOcc $adv.maxOcc
-            #end if
             $adv.initUniform
             $adv.noFragLengthDist
             $adv.noBiasLengthThreshold
@@ -186,7 +185,7 @@
                 --geneMap ./geneMap.${geneMap.ext}
             #end if
             $adv.noEffectiveLengthCorrection
-            $adv.useVBOpt
+            $adv.useEM
             #if str($adv.numBiasSamples):
                 --numBiasSamples $adv.numBiasSamples
             #end if
@@ -202,11 +201,21 @@
             #if str($adv.numBootstraps):
                 --numBootstraps $adv.numBootstraps
             #end if
+            #if str($adv.consensusSlack):
+                --consensusSlack $adv.consensusSlack
+            #else:
+                #if $quasi_orphans.validateMappings:
+                    --consensusSlack 1
+                #else:
+                    --consensusSlack 0
+                #end if
+            #end if
             $adv.perTranscriptPrior
             #if $adv.vbPrior:
                 --vbPrior $adv.vbPrior
             #end if
             $adv.writeUnmappedNames
+            --sigDigits $adv.sigDigits
             #if str($adv.writeMappings):
                 $adv.writeMappings > ${output_sam}
             #end if
@@ -263,21 +272,31 @@
         <conditional name="quasi_orphans">
             <param argument="--type" type="select" label="Type of index" help="When using quasi, orphaned reads will be considered when performing lightweight-alignment.">
                 <option value="quasi" selected="True">quasi</option>
-                <option value="fmd">fmd</option>
             </param>
             <when value="quasi">
+                <param argument="--validateMappings" type="boolean" truevalue="--validateMappings" falsevalue="" checked="False"
+                label="Validate mappings"
+                help="Validate mappings using alignment-based verifcation. If this flag is passed, quasi-mappings will be validated to ensure that they could give rise to a reasonable alignment before they are further used for quantification."/>
+                <param name="matchScore" argument="--ma" type="integer" value="2"
+                label="Match Score"
+                help="The value given to a match between read and reference nucleotides in an alignment."/>
+                <param name="mismatchPenalty" argument="--mp" type="integer" value="4"
+                label="Mismatch Penalty"
+                help="The value given to a mis-match between read and reference nucleotides in an alignment. This will be cast to a negative value."/>
+                <param name="gapOpenPenalty" argument="--go" type="integer" value="5"
+                label="Gap Open Penalty"
+                help="The value given to a gap opening in an alignment."/>
+                <param name="gapExtensionPenalty" argument="--ge" type="integer" value="3"
+                label="Gap Extension Penalty"
+                help="The value given to a gap extension in an alignment."/>
+                <param argument="--minScoreFraction" type="float" value="0.65" min="0.0" max="0.99"
+                label="Min Score Fraction"
+                help="The fraction of the optimal possible alignment score that a mapping must achieve in order to be considered valid. Should be in (0,1]."/>
             </when>  <!-- build-in -->
-            <when value="fmd">
-                <param argument="--allowOrphans" type="boolean" truevalue="--allowOrphans" falsevalue="" checked="True"
-                    label="Consider orphaned reads as valid hits when performing lightweight-alignment"
-                    help="This option will increase sensitivity (allow more reads to map and more transcripts to be detected), but may decrease specificity as orphaned alignments are more likely to be spurious."/>
-            </when>  <!-- history -->
         </conditional>
         <param argument="--perfectHash" type="boolean" truevalue="--perfectHash" falsevalue="" checked="False"
             label="Perfect Hash"
             help="Build the index using a perfect hash rather than a dense hash.  This will require  less memory (especially during quantification), but will take longer to construct "/>
-        <param argument="--sasamp" type="integer" value="1" optional="True" label="Suffix Array"
-            help="The interval at which the suffix array should be sampled. Smaller values are faster, but produce a larger index. The default should be OK, unless your transcriptome is huge. This value should be a power of 2."/>
         <param argument="--seqBias" type="boolean" truevalue="--seqBias" falsevalue="" checked="False"
             label="Perform sequence-specific bias correction"
             help=""/>
@@ -287,6 +306,9 @@
         <param argument="--geneMap" type="data" format="tabular,gff,gtf" optional="True"
             label="File containing a mapping of transcripts to genes" 
             help="If this file is provided Salmon will output both quant.sf and quant.genes.sf files, where the latter contains aggregated gene-level abundance estimates. The transcript to gene mapping should be provided as either a GTF file, or a in a simple tab-delimited format where each line contains the name of a transcript and the gene to which it belongs separated by a tab." />
+        <param argument="--noErrorModel" type="boolean" truevalue="--noErrorModel" falsevalue="" checked="False"
+            label="No Error Model"
+            help="Turn off the alignment error model, which takes into account the the observed frequency of different types of mismatches / indels when computing the likelihood of a given alignment. Turning this off can speed up alignment-based salmon, but can harm quantification accuracy."/>
         <section name="adv" title="Additional Options">
             <param argument="--writeMappings" type="boolean" truevalue="--writeMappings" falsevalue="" checked="False"
                 label="Write Mappings"
@@ -329,9 +351,6 @@
             <param argument="--forgettingFactor" type="float" value="0.65000000000000002" optional="True"
                 label="The forgetting factor used in the online learning schedule."
                 help=" A smaller value results in quicker learning, but higher variance and may be unstable. A larger value results in slower learning but may be more stable.  Value should be in the interval (0.5, 1.0]." />
-            <param argument="--maxOcc" type="integer" value="200" optional="True"
-                label="(S)MEMs occuring more than this many times won't be considered"
-                help=""/>
             <param argument="--initUniform" type="boolean" truevalue="--initUniform" falsevalue="" checked="False"
                 label="Initialization with uniform parameters"
                 help="initialize the offline inference with uniform parameters, rather than seeding with online parameters." />
@@ -346,7 +365,7 @@
                 help="[experimental] : Don't consider concordance with the learned fragment length distribution when trying to determine the probability that a fragment has originated from a specified location.  Normally, Fragments with unlikely lengths will be assigned a smaller relative probability than those with more likely lengths. When this flag is passed in, the observed fragment length has no effect on that fragment's a priori probability." />
             <param argument="--noBiasLengthThreshold" type="boolean" truevalue="--noBiasLengthThreshold" falsevalue="" checked="False"
                 label="[experimental] : If this option is enabled, then no (lower) threshold will be set on how short bias correction can make effecctive lengths."
-                help="This can increase the precision of bias correction, but harm robustness. The difault correction applies a threshold." />
+                help="This can increase the precision of bias correction, but harm robustness. The default correction applies a threshold." />
             <param argument="--numBiasSamples" type="integer" value="2000000" optional="True"
                 label="Number of fragment mappings to use when learning the sequence-specific bias model."
                 help="" />
@@ -362,8 +381,8 @@
             <param argument="--splitSpanningSeeds" type="boolean" truevalue="--splitSpanningSeeds" falsevalue="" checked="False"
                 label="Attempt to split seeds that happen to fall on the boundary between two transcripts."
                 help="This can improve the fragment hit-rate, but is usually not necessary."/>
-            <param argument="--useVBOpt" type="boolean" truevalue="--useVBOpt" falsevalue="" checked="False"
-                label="Use the Variational Bayesian EM rather than the traditional EM algorithm for optimization in the batch passes."
+            <param argument="--useEM" type="boolean" truevalue="--useEM" falsevalue="" checked="False"
+                label="Use the traditional EM algorithm for optimization in the batch passes."
                 help=""/>
             <param argument="--numGibbsSamples" type="integer" value="0" optional="True"
                 label=" Number of Gibbs sampling rounds to perform."
@@ -380,6 +399,12 @@
             <param argument="--writeUnmappedNames" type="boolean" truevalue="--writeUnmappedNames" falsevalue="" checked="False"
                 label="Write the names of un-mapped reads to the file unmapped_names.txt."
                 help=""/>
+            <param argument="--sigDigits" type="integer" value="3"
+                label="Significant Digits"
+                help="The number of significant digits to write when outputting the EffectiveLength and NumReads columns."/>
+            <param argument="--consensusSlack" type="integer" optional="True"
+                label="Consensus Slack"
+                help="The amount of slack allowed in the quasi-mapping consensus mechanism.  Normally, a transcript must cover all hits to be considered for mapping. If this is set to a value, X, greater than 0, then a transcript can fail to cover up to X hits before it is discounted as a mapping candidate.  The default value of this option is 1 if --validateMappings is given and 0 otherwise."/>
         </section>
     </inputs>
 
@@ -572,6 +597,150 @@
                 </assert_contents>
             </output>
         </test>
+        <test>
+            <param name="single_or_paired_opts" value="paired" />
+            <param name="input_mate1" value="reads_1.fastq" />
+            <param name="input_mate2" value="reads_2.fastq" />
+            <param name="TranscriptSource" value="history" />
+            <param name="ownFile" value="transcripts.fasta" ftype="fasta" />
+            <param name="geneMap" value="gene_map.tab" ftype="tabular" />
+            <param name="validateMappings" value="True" />
+            <output name="output_quant">
+                <assert_contents>
+                    <has_text text="EffectiveLength" />
+                    <has_text text="TPM" />
+                    <has_text text="NM_001168316" />
+                    <has_text text="NM_174914" />
+                    <has_text text="NM_018953" />
+                    <has_text text="NR_003084" />
+                    <has_text text="NM_017410" />
+                    <has_text text="NM_153693" />
+                    <has_text text="NR_031764" />
+                    <has_n_columns n="5" />
+                </assert_contents>
+            </output>
+            <output name="output_gene_quant">
+                <assert_contents>
+                    <has_text text="EffectiveLength" />
+                    <has_text text="TPM" />
+                    <has_text text="baz" />
+                    <has_text text="bar" />
+                    <has_text text="2283" />
+                    <has_text text="1640" />
+                    <has_n_columns n="5" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="single_or_paired_opts" value="paired_collection" />
+            <param name="input_1">
+                <collection type="paired">
+                    <element name="forward" value="reads_1.fastq" ftype="fastqsanger" />
+                    <element name="reverse" value="reads_2.fastq" ftype="fastqsanger" />
+                </collection>    
+            </param> 
+            <param name="TranscriptSource" value="history" />
+            <param name="ownFile" value="transcripts.fasta" ftype="fasta" />
+            <param name="geneMap" value="gene_map.tab" ftype="tabular" />
+            <param name="validateMappings" value="True" />
+            <output name="output_quant">
+                <assert_contents>
+                    <has_text text="EffectiveLength" />
+                    <has_text text="TPM" />
+                    <has_text text="NM_001168316" />
+                    <has_text text="NM_174914" />
+                    <has_text text="NM_018953" />
+                    <has_text text="NR_003084" />
+                    <has_text text="NM_017410" />
+                    <has_text text="NM_153693" />
+                    <has_text text="NR_031764" />
+                    <has_n_columns n="5" />
+                </assert_contents>
+            </output>
+            <output name="output_gene_quant">
+                <assert_contents>
+                    <has_text text="EffectiveLength" />
+                    <has_text text="TPM" />
+                    <has_text text="baz" />
+                    <has_text text="bar" />
+                    <has_text text="2283" />
+                    <has_text text="1640" />
+                    <has_n_columns n="5" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="single_or_paired_opts" value="paired" />
+            <param name="input_mate1" value="reads_1.fastq" />
+            <param name="input_mate2" value="reads_2.fastq" />
+            <param name="TranscriptSource" value="history" />
+            <param name="ownFile" value="transcripts.fasta" ftype="fasta" />
+            <param name="geneMap" value="gene_map.tab" ftype="tabular" />
+            <param name="useEM" value="True" />
+            <output name="output_quant">
+                <assert_contents>
+                    <has_text text="EffectiveLength" />
+                    <has_text text="TPM" />
+                    <has_text text="NM_001168316" />
+                    <has_text text="NM_174914" />
+                    <has_text text="NM_018953" />
+                    <has_text text="NR_003084" />
+                    <has_text text="NM_017410" />
+                    <has_text text="NM_153693" />
+                    <has_text text="NR_031764" />
+                    <has_n_columns n="5" />
+                </assert_contents>
+            </output>
+            <output name="output_gene_quant">
+                <assert_contents>
+                    <has_text text="EffectiveLength" />
+                    <has_text text="TPM" />
+                    <has_text text="baz" />
+                    <has_text text="bar" />
+                    <has_text text="2283" />
+                    <has_text text="1640" />
+                    <has_n_columns n="5" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="single_or_paired_opts" value="paired_collection" />
+            <param name="input_1">
+                <collection type="paired">
+                    <element name="forward" value="reads_1.fastq" ftype="fastqsanger" />
+                    <element name="reverse" value="reads_2.fastq" ftype="fastqsanger" />
+                </collection>    
+            </param> 
+            <param name="TranscriptSource" value="history" />
+            <param name="ownFile" value="transcripts.fasta" ftype="fasta" />
+            <param name="geneMap" value="gene_map.tab" ftype="tabular" />
+            <param name="useEM" value="True" />
+            <output name="output_quant">
+                <assert_contents>
+                    <has_text text="EffectiveLength" />
+                    <has_text text="TPM" />
+                    <has_text text="NM_001168316" />
+                    <has_text text="NM_174914" />
+                    <has_text text="NM_018953" />
+                    <has_text text="NR_003084" />
+                    <has_text text="NM_017410" />
+                    <has_text text="NM_153693" />
+                    <has_text text="NR_031764" />
+                    <has_n_columns n="5" />
+                </assert_contents>
+            </output>
+            <output name="output_gene_quant">
+                <assert_contents>
+                    <has_text text="EffectiveLength" />
+                    <has_text text="TPM" />
+                    <has_text text="baz" />
+                    <has_text text="bar" />
+                    <has_text text="2283" />
+                    <has_text text="1640" />
+                    <has_n_columns n="5" />
+                </assert_contents>
+            </output>
+        </test>
     </tests>
 
     <help><![CDATA[