| Previous changeset 0:d35cb34f2b85 (2019-07-01) Next changeset 2:1d839ead7ad3 (2020-07-15) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4" |
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modified:
macros.xml macros_process.xml stacks_gstacks.xml |
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added:
test-data/procrad/process_radtags2.out |
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| diff -r d35cb34f2b85 -r 27359c6bf3e3 macros.xml --- a/macros.xml Mon Jul 01 10:59:14 2019 -0400 +++ b/macros.xml Mon Sep 30 14:19:17 2019 -0400 |
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| @@ -8,7 +8,7 @@ </xml> <token name="@STACKS_VERSION@">2.4</token> - <token name="@WRAPPER_VERSION@">0</token> + <token name="@WRAPPER_VERSION@">1</token> <!-- fix to 18.01 since https://github.com/galaxyproject/galaxy/pull/7032 --> <token name="@PROFILE@">18.01</token> @@ -216,8 +216,8 @@ </expand> </xml> - <!-- fastq input (used in denovomap, tsv2bam, ustacks) - - fastq_optional: makes fastq input optional (true/false) + <!-- fastq input (used in denovomap, tsv2bam, ustacks) + - fastq_optional: makes fastq input optional (true/false) - se_option: wording for "single end" option (for tsv2bam this is the reverse reads for the others its the forward reads) - help: help text --> @@ -568,10 +568,10 @@ </expand> </xml> - <!-- variant calling option for use in gstacks and denovomap + <!-- variant calling option for use in gstacks and denovomap default for var_alpha is 0.01 if model == marukilow (which is the case in denovomap and refmap) otherwise no default is is available and gstacks will output and error - "Error: No value was provided for \-\-var-alpha and there is no default for this model)" + "Error: No value was provided for \-\-var-alpha and there is no default for this model)" --> <xml name="variant_calling_options_vg" token_varalpha_default=""> <param argument="--var-alpha" name="var_alpha" type="float" value="@VARALPHA_DEFAULT@" min="0" label="Alpha threshold for discovering SNPs" help="Default is 0.01 if the marukilow model is used (which is the case in refmap and denovomap), otherwise no default value is available." /> |
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| diff -r d35cb34f2b85 -r 27359c6bf3e3 macros_process.xml --- a/macros_process.xml Mon Jul 01 10:59:14 2019 -0400 +++ b/macros_process.xml Mon Sep 30 14:19:17 2019 -0400 |
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| @@ -75,7 +75,7 @@ <param name="score" type="integer" value="10" min="0" max="40" argument="-s" label="Set the score limit. If the average score within the sliding window drops below this value, the read is discarded" /> <param name="remove" type="boolean" checked="false" truevalue="-c" falsevalue="" argument="-c" label="Clean data, remove any read with an uncalled base" /> <param name="discard" type="boolean" checked="false" truevalue="-q" falsevalue="" argument="-q" label="Discard reads with low quality scores"/> - <param argument="--filter_illumina" type="boolean" checked="false" truevalue="--filter_illumina" falsevalue="" label="Discard reads that have been marked by Illumina's chastity/purity filter as failing" /> + <param argument="--filter-illumina" name="filter_illumina" type="boolean" checked="false" truevalue="--filter-illumina" falsevalue="" label="Discard reads that have been marked by Illumina's chastity/purity filter as failing" /> </when> <when value="no"> <param argument="--len_limit" type="integer" value="" optional="true" label="Minimum sequence length" help="useful if your data has already been trimmed"/> |
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| diff -r d35cb34f2b85 -r 27359c6bf3e3 stacks_gstacks.xml --- a/stacks_gstacks.xml Mon Jul 01 10:59:14 2019 -0400 +++ b/stacks_gstacks.xml Mon Sep 30 14:19:17 2019 -0400 |
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| @@ -11,6 +11,14 @@ @FASTQ_INPUT_FUNCTIONS@ mkdir bam_inputs stacks_outputs && + +## annoyingly gstacks creates stacks_output/gstacks.log +## instead of just writing to stderr as the other tools +## hence we do not use the tokens and return populations.log as log file and take the stderr +#if $output_log + ln -s '$output_log' stacks_outputs/gstacks.log && +#end if + #if $mode_cond.mode_select == "denovo" and not $popmap: ## since collections have no len .. yet #try: @@ -88,14 +96,6 @@ #end if #end if - -## annoyingly gstacks creates stacks_output/gstacks.log -## instead of just writing to stderr as the other tools -## hence we do not use the tokens and return populations.log as log file and take the stderr -#if $output_log - && mv stacks_outputs/gstacks.log $output_log -#end if - @EXTRACT_VCF@ ## TODO extract individual distributions from stacks_outputs/gstacks.log.distribs @@ -250,7 +250,6 @@ <param name="add_log" value="yes" /> <assert_command> <has_text text="--ignore-pe-reads" /> - <has_text text="--rm-pcr-duplicates" /> <has_text text="--kmer-length 23" /> <has_text text="--max-debruijn-reads 666" /> <has_text text="--min-kmer-cov 3" /> @@ -270,15 +269,15 @@ <param name="mode_select" value="refbased"/> <conditional name="paired_cond"> <param name="paired_select" value=""/> - <!--<param name="rm_unpaired_reads" value="\-\-rm-unpaired-reads" /> removes to much of the test data and gstacks fails--> + <!--<param name="rm_unpaired_reads" value="\-\-rm-unpaired-reads" /> removes too much of the test data and gstacks fails--> <param name="rm_pcr_duplicates" value="--rm-pcr-duplicates" /> </conditional> </conditional> <param name="add_log" value="yes" /> <assert_command> - <has_text text="-I bam_inputs" /> - <not_has_text text="-B " /> - <has_text text="--rm-unpaired-reads" /> + <not_has_text text="-I bam_inputs" /> + <has_text text="-B " /> + <not_has_text text="--rm-unpaired-reads" /> <has_text text="--rm-pcr-duplicates" /> </assert_command> </test> @@ -296,7 +295,7 @@ <param name="min_mapq" value="23" /> <param name="max_clipped" value="0.23" /> <param name="max_insert_len" value="666" /> - <param name="details" value="--detailed"/> + <param name="details" value="--details"/> <param name="phasing_cooccurrences_thr_min" value="2"/> <param name="phasing_cooccurrences_thr_max" value="3"/> <param name="phasing_dont_prune_hets" value="--phasing-dont-prune-hets" /> @@ -307,13 +306,13 @@ <param name="model_cond|var_alpha" value="0.1" /> <param name="add_log" value="yes" /> <assert_command> - <not_has_text text="-I bam_inputs" /> - <has_text text="-B " /> + <has_text text="-I bam_inputs" /> + <not_has_text text="-B " /> <has_text text="--unpaired" /> <has_text text="--min-mapq 23" /> <has_text text="--max-clipped 0.23" /> <has_text text="--max-insert-len 666" /> - <has_text text="--detailed" /> + <has_text text="--details" /> <has_text text="--phasing-cooccurrences-thr-range 2,3" /> <has_text text="--phasing-dont-prune-hets" /> <has_text text="--model snp" /> @@ -333,8 +332,8 @@ </conditional> <param name="add_log" value="yes" /> <assert_command> - <has_text text="-I bam_inputs" /> - <not_has_text text="-B " /> + <not_has_text text="-I bam_inputs" /> + <has_text text="-B " /> <has_text text="--ignore-pe-reads" /> </assert_command> <output name="output_log"><assert_contents><has_text text="gstacks is done." /></assert_contents></output> |
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| diff -r d35cb34f2b85 -r 27359c6bf3e3 test-data/procrad/process_radtags2.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/procrad/process_radtags2.out Mon Sep 30 14:19:17 2019 -0400 |
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| @@ -0,0 +1,88 @@ +process_radtags v2.4, executed 2019-09-30 14:57:00 (zlib-1.2.11) +process_radtags -p stacks_inputs/ -i gzfastq -b /tmp/tmpe_shit/files/d/e/d/dataset_ded45538-15ef-471f-9585-07ee09b6e6d4.dat --inline_null -y gzfastq -o stacks_outputs -w 0.1 -s 11 -c -q -D -e ecoRI +File Retained Reads Low Quality Barcode Not Found RAD cutsite Not Found Total +R1.fastq.gz 2222 0 0 4778 7000 +R2.fastq.gz 0 0 7000 0 7000 + +Total Sequences 14000 +Barcode Not Found 7000 +Low Quality 0 +RAD Cutsite Not Found 4778 +Retained Reads 2222 + +Barcode Filename Total NoRadTag LowQuality Retained +ATGGGG PopA_01 160 94 0 66 +GGGTAA PopA_02 146 86 0 60 +AGGAAA PopA_03 224 132 0 92 +TTTAAG PopA_04 168 146 0 22 +GGTGTG PopA_05 220 154 0 66 +TGATGT PopA_06 214 147 0 67 +GGTTGT PopA_07 182 137 0 45 +ATAAGT PopA_08 232 164 0 68 +AAGATA PopA_09 182 134 0 48 +TGTGAG PopA_10 168 128 0 40 +ATAGTT PopA_11 200 132 0 68 +GGAAGG PopA_12 178 136 0 42 +TTTGTG PopA_13 190 152 0 38 +TTAAAT PopA_14 166 96 0 70 +AATAAG PopA_15 152 74 0 78 +AAGAGG PopA_16 174 112 0 62 +TAGTGT PopA_17 242 146 0 96 +TGGAAG PopA_18 148 98 0 50 +GGGTTG PopA_19 110 64 0 46 +CATCAT PopA_20 178 144 0 34 +GGAGAG PopB_20 210 142 0 68 +GTTTTA PopB_01 136 90 0 46 +TGATAA PopB_02 166 108 0 58 +GTTGAT PopB_03 148 74 0 74 +AGATTA PopB_04 180 156 0 24 +GTATAG PopB_05 136 106 0 30 +TTGGGA PopB_06 166 112 0 54 +ATATAT PopB_07 242 156 0 86 +GATGAG PopB_08 208 152 0 56 +GGGAAT PopB_09 198 126 0 72 +AGTAAT PopB_10 164 120 0 44 +GGGATA PopB_11 146 90 0 56 +GAGAAG PopB_12 162 110 0 52 +AGTAGA PopB_13 204 146 0 58 +AAGGAT PopB_14 180 128 0 52 +AGGGTA PopB_15 134 72 0 62 +TGTTTT PopB_16 138 98 0 40 +ATGATG PopB_17 142 100 0 42 +GAGTTA PopB_18 160 112 0 48 +ATGTAG PopB_19 146 104 0 42 + +Sequences not recorded +Barcode Total +CCGGTG 772 +CCGCGC 750 +CCGACA 743 +CCGGTC 723 +CCGCCT 695 +CCGTGG 675 +CCGGTT 667 +CCGATC 579 +CCGTGT 417 +CCGTAT 252 +CCGCGT 198 +CCGCGG 150 +CCGCAT 117 +CCGTTC 94 +CCGTAC 38 +CCGGGA 32 +CCGGAG 26 +CCGAAC 24 +CCGAGT 18 +CCGTGA 10 +CCGGGT 7 +CCGCTT 2 +CCGACG 2 +CCGATT 1 +CCGCCC 1 +CCGGCA 1 +CCGGCT 1 +CCGGGG 1 +CCGCCG 1 +CCGTGC 1 +CCGTAG 1 +CCGACT 1 |