Mercurial > repos > bgruening > salmon
diff salmon.xml @ 6:885d11dc8090 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86
| author | bgruening |
|---|---|
| date | Thu, 10 May 2018 06:48:28 -0400 |
| parents | 53e9709776a0 |
| children | e7e885f718fb |
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--- a/salmon.xml Wed Jul 12 14:05:10 2017 -0400 +++ b/salmon.xml Thu May 10 06:48:28 2018 -0400 @@ -10,12 +10,20 @@ <option value="SR">read 1 (or single-end read) comes from the reverse strand (SR)</option> </param> </xml> - <token name="@VERSION@">0.8.2</token> + <xml name="orientation"> + <param name="orientation" type="select" label="Relative orientation of reads within a pair"> + <option value="M">Mates are oriented in the same direction (M = matching)</option> + <option value="O">Mates are oriented away from each other (O = outward)</option> + <option value="I" selected="True">Mates are oriented toward each other (I = inward)</option> + </param> + </xml> + <token name="@VERSION@">0.9.1</token> </macros> <requirements> <requirement type="package" version="1.0.6">bzip2</requirement> <requirement type="package" version="@VERSION@">salmon</requirement> + <requirement type="package" version="1.2">seqtk</requirement> </requirements> <stdio> @@ -52,27 +60,52 @@ #if $single_or_paired.input_singles.ext == 'fasta': #set $ext = 'fasta' #else: - #if $single_or_paired.input_singles.is_of_type('fastq.gz'): + #if $single_or_paired.input_singles.is_of_type("fastq.gz", "fastqsanger.gz"): #set compressed = 'GZ' - #else if $single_or_paired.input_singles.is_of_type('fastq.bz2'): + #else if $single_or_paired.input_singles.is_of_type("fastq.bz2", "fastqsanger.bz2"): #set compressed = 'BZ2' #end if #set $ext = 'fastq' #end if ln -s $single_or_paired.input_singles ./single.$ext && - #else: + #else if $single_or_paired.single_or_paired_opts == 'paired': #if $single_or_paired.input_mate1.ext == 'fasta': #set $ext = 'fasta' #else: - #if $single_or_paired.input_mate1.is_of_type('fastq.gz'): + #if $single_or_paired.input_mate1.is_of_type("fastq.gz", "fastqsanger.gz"): #set compressed = 'GZ' - #else if $single_or_paired.input_mate1.is_of_type('fastq.bz2'): + #else if $single_or_paired.input_mate1.is_of_type("fastq.bz2", "fastqsanger.bz2"): #set compressed = 'BZ2' #end if #set $ext = 'fastq' #end if ln -s $single_or_paired.input_mate1 ./mate1.$ext && ln -s $single_or_paired.input_mate2 ./mate2.$ext && + #else if $single_or_paired.single_or_paired_opts == 'paired_collection': + #if $single_or_paired.input_1.forward.ext == 'fasta': + #set $ext = 'fasta' + #else: + #if $single_or_paired.input_1.forward.is_of_type("fastq.gz", "fastqsanger.gz"): + #set compressed = 'GZ' + #else if $single_or_paired.input_1.forward.is_of_type("fastq.bz2", "fastqsanger.bz2"): + #set compressed = 'BZ2' + #end if + #set $ext = 'fastq' + #end if + ln -s ${single_or_paired.input_1.forward} ./mate1.$ext && + ln -s ${single_or_paired.input_1.reverse} ./mate2.$ext && + #else if $single_or_paired.single_or_paired_opts == 'paired_interleaved': + #if $single_or_paired.input_1.ext == 'fasta': + #set $ext = 'fasta' + #else: + #if $single_or_paired.input_1.is_of_type("fastq.gz", "fastqsanger.gz"): + #set compressed = 'GZ' + #else if $single_or_paired.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"): + #set compressed = 'BZ2' + #end if + #set $ext = 'fastq' + #end if + ln -s $single_or_paired.input_1 ./mate1.$ext && #end if #if $geneMap: ln -s "$geneMap" ./geneMap.${geneMap.ext} && @@ -82,22 +115,32 @@ #if $single_or_paired.single_or_paired_opts == 'single': --libType ${single_or_paired.strandedness} #if $compressed == 'GZ': - --unmatedReads <(zcat ./single.$ext) + --unmatedReads <(zcat < ./single.$ext) #else if $compressed == 'BZ2': - --unmatedReads <(bzcat ./single.$ext) + --unmatedReads <(bzcat < ./single.$ext) #else: --unmatedReads ./single.$ext #end if #else: - #if $compressed == 'GZ': - --mates1 <(zcat ./mate1.$ext) - --mates2 <(zcat ./mate2.$ext) - #else if $compressed == 'BZ2': - --mates1 <(bzcat ./mate1.$ext) - --mates2 <(bzcat ./mate2.$ext) + #if $single_or_paired.single_or_paired_opts == 'paired_interleaved': + #if $compressed == 'BZ2': + --mates1 <(bzcat < ./mate1.$ext | seqtk seq -1) + --mates2 <(bzcat < ./mate1.$ext | seqtk seq -2) + #else: + --mates1 <(seqtk seq -1 ./mate1.$ext) + --mates2 <(seqtk seq -2 ./mate1.$ext) + #end if #else: - --mates1 ./mate1.$ext - --mates2 ./mate2.$ext + #if $compressed == 'GZ': + --mates1 <(zcat < ./mate1.$ext) + --mates2 <(zcat < ./mate2.$ext) + #else if $compressed == 'BZ2': + --mates1 <(bzcat < ./mate1.$ext) + --mates2 <(bzcat < ./mate2.$ext) + #else: + --mates1 ./mate1.$ext + --mates2 ./mate2.$ext + #end if #end if --libType "${single_or_paired.orientation}${single_or_paired.strandedness}" #end if @@ -113,9 +156,7 @@ --incompatPrior $adv.incompatPrior $adv.consistentHits $adv.dumpEq - #if str($adv.gcSizeSamp): - --gcSizeSamp $adv.gcSizeSamp - #end if + $adv.reduceGCMemory #if str($adv.biasSpeedSamp): --biasSpeedSamp $adv.biasSpeedSamp #end if @@ -195,21 +236,29 @@ <param name="single_or_paired_opts" type="select" label="Is this library mate-paired?"> <option value="single">Single-end</option> <option value="paired">Paired-end</option> + <option value="paired_collection">Paired-end Dataset Collection</option> + <option value="paired_interleaved">Paired-end data from single interleaved dataset</option> </param> <when value="single"> - <param name="input_singles" type="data" format="fastq,fasta,fastq.gz" label="FASTQ/FASTA file" help="FASTQ file." /> + <param name="input_singles" type="data" format="fastq,fasta,fastq.gz,fastq.bz2" label="FASTQ/FASTA file" help="FASTQ file." /> <expand macro="strandedness" /> </when> <when value="paired"> - <param name="input_mate1" type="data" format="fastq,fasta,fastq.gz" label="Mate pair 1" help="FASTQ file." /> - <param name="input_mate2" type="data" format="fastq,fasta,fastq.gz" label="Mate pair 2" help="FASTQ file." /> - <param name="orientation" type="select" label="Relative orientation of reads within a pair"> - <option value="M">Mates are oriented in the same direction (M = matching)</option> - <option value="O">Mates are oriented away from each other (O = outward)</option> - <option value="I" selected="True">Mates are oriented toward each other (I = inward)</option> - </param> + <param name="input_mate1" type="data" format="fastq,fasta,fastq.gz,fastq.bz2,fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="Mate pair 1" help="FASTQ file." /> + <param name="input_mate2" type="data" format="fastq,fasta,fastq.gz,fastq.bz2,fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="Mate pair 2" help="FASTQ file." /> + <expand macro="orientation" /> <expand macro="strandedness" /> </when> + <when value="paired_collection"> + <param name="input_1" format="fastq,fasta,fastq.gz,fastq.bz2,fastqsanger,fastqsanger.gz,fastqsanger.bz2" type="data_collection" collection_type="paired" label="FASTQ Paired Dataset" help="Must be of datatype "fastqsanger" or "fasta"" /> + <expand macro="orientation" /> + <expand macro="strandedness" /> + </when> + <when value="paired_interleaved"> + <param name="input_1" format="fastq,fasta,fastq.gz,fastq.bz2,fastqsanger,fastqsanger.gz,fastqsanger.bz2" type="data" label="Interleaved FASTQ file" help="Must be of datatype "fastqsanger" or "fasta". --interleaved"/> + <expand macro="orientation" /> + <expand macro="strandedness" /> + </when> </conditional> <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."> @@ -247,8 +296,9 @@ help="This option sets the prior probability that an alignment that disagrees with the specified library type (--libType) results from the true fragment origin. Setting this to 0 specifies that alignments that disagree with the library type should be 'impossible', while setting it to 1 says that alignments that disagree with the library type are no less likely than those that do" /> <param argument="--dumpEq" type="boolean" truevalue="--dumpEq" falsevalue="" checked="False" label="Dump the equivalence class counts that were computed during quasi-mapping." help=""/> - <param argument="--gcSizeSamp" type="integer" value="1" optional="True" - label="The value by which to down-sample transcripts when representing the GC content" help="Larger values will reduce memory usage, but may decrease the fidelity of bias modeling results."/> + <param argument="--reduceGCMemory" type="boolean" truevalue="--reduceGCMemory" falsevalue="" optional="True" checked="False" + label="If this option is selected, a more memory efficient (but slightly slower representation is used to compute fragment GC content." + help="Enabling this will reduce memory usage, but can also reduce speed. However, the results themselves will remain the same."/> <param argument="--biasSpeedSamp" type="integer" value="1" optional="True" label="The value at which the fragment length PMF is down-sampled when evaluating GC fragment bias." help="Larger values speed up effective length correction, but may decrease the fidelity of bias modeling results."/> <param argument="--strictIntersect" type="boolean" truevalue="--strictIntersect" falsevalue="" checked="False" @@ -388,6 +438,70 @@ </assert_contents> </output> </test> + <test> <!-- bzipped input --> + <param name="single_or_paired_opts" value="paired" /> + <param name="input_mate1" value="reads_1.fastq.bz2" ftype="fastqsanger.bz2" /> + <param name="input_mate2" value="reads_2.fastq.bz2" ftype="fastqsanger.bz2" /> + <param name="biasCorrect" value="False" /> + <param name="TranscriptSource" value="history" /> + <param name="ownFile" value="transcripts.fasta" ftype="fasta" /> + <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> + </test> + <test> <!-- interleaved bz2 input --> + <param name="single_or_paired_opts" value="paired_interleaved" /> + <param name="input_1" value="reads_both.fastq.bz2" ftype="fastqsanger.bz2" /> + <param name="biasCorrect" value="False" /> + <param name="TranscriptSource" value="history" /> + <param name="ownFile" value="transcripts.fasta" ftype="fasta" /> + <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> + </test> + <test> <!-- interleaved gz input --> + <param name="single_or_paired_opts" value="paired_interleaved" /> + <param name="input_1" value="reads_both.fastq.gz" ftype="fastqsanger.gz" /> + <param name="biasCorrect" value="False" /> + <param name="TranscriptSource" value="history" /> + <param name="ownFile" value="transcripts.fasta" ftype="fasta" /> + <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> + </test> <test> <param name="single_or_paired_opts" value="paired" /> <param name="input_mate1" value="reads_1.fastq" /> @@ -421,6 +535,43 @@ </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" /> + <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[