| Previous changeset 0:6fba323a242d (2019-07-01) Next changeset 2:38942a7e3801 (2020-02-12) |
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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_populations.xml |
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added:
test-data/procrad/process_radtags2.out |
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| diff -r 6fba323a242d -r 9a44832748c5 macros.xml --- a/macros.xml Mon Jul 01 11:01:14 2019 -0400 +++ b/macros.xml Mon Sep 30 14:17:47 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 6fba323a242d -r 9a44832748c5 macros_process.xml --- a/macros_process.xml Mon Jul 01 11:01:14 2019 -0400 +++ b/macros_process.xml Mon Sep 30 14:17:47 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 6fba323a242d -r 9a44832748c5 stacks_populations.xml --- a/stacks_populations.xml Mon Jul 01 11:01:14 2019 -0400 +++ b/stacks_populations.xml Mon Sep 30 14:17:47 2019 -0400 |
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| @@ -8,9 +8,11 @@ <command detect_errors="aggressive"><![CDATA[ #import re -mkdir stacks_inputs stacks_outputs +mkdir stacks_inputs stacks_outputs && -&& +#if $output_log + ln -s '$output_log' stacks_outputs/populations.log && +#end if #if str($options_usage.input_type) == 'stacks' #for $input_file in $options_usage.input_aln @@ -45,9 +47,9 @@ ## Data filtering --p $options_filtering.minpop --r $options_filtering.minperc --R $options_filtering.min_samples_overall +--min-populations $options_filtering.minpop +--min-samples-per-pop $options_filtering.minperc +--min-samples-overall $options_filtering.min_samples_overall $options_filtering.filter_haplotype_wise --min_maf $options_filtering.min_maf --min_mac $options_filtering.min_mac @@ -143,10 +145,6 @@ > $output_log #end if && find stacks_outputs -type f -iname "input.p*" | while read file; do mv "\$file" "\$(echo \$file | sed 's/\/input.p/\/populations/;')"; done -#else - #if $output_log - && mv stacks_outputs/populations.log $output_log - #end if #end if ]]></command> @@ -169,8 +167,8 @@ <!-- Data Filtering --> <section name="options_filtering" title="Data filtering options" expanded="true"> - <param name="minperc" argument="-r" type="float" value="0.0" min="0" max="1" label="Minimum percentage of individuals in a population required to process a locus for that population" /> - <param name="minpop" argument="-p" type="integer" value="1" label="Minimum number of populations a locus must be present in to process a locus" /> + <param name="minperc" argument="--min-samples-per-pop" type="float" value="0.0" min="0" max="1" label="Minimum percentage of individuals in a population required to process a locus for that population" /> + <param name="minpop" argument="--min-populations" type="integer" value="1" label="Minimum number of populations a locus must be present in to process a locus" /> <param name="min_samples_overall" argument="--min-samples-overall" type="float" value="0.0" min="0" max="1" label="minimum percentage of individuals across populations required to process a locus" /> <param name="filter_haplotype_wise" argument="--filter-haplotype-wise" type="boolean" truevalue="--filter-haplotype-wise" falsevalue="" checked="false" label="apply the above filters haplotype wise" help="unshared SNPs will be pruned to reduce haplotype-wise missing data." /> <param argument="--min_maf" type="float" value="0" min="0" max="0.5" label="Minimum minor allele frequency" help="specify a minimum minor allele frequency required to process a nucleotide site at a locus" /> @@ -431,8 +429,8 @@ <param name="blacklist" value="populations/blacklist.tsv" ftype="tabular" /> </section> <assert_command> - <has_text text="-r 0.1" /> - <has_text text="-p 2" /> + <has_text text="--min-samples-per-pop 0.1" /> + <has_text text="--min-populations 2" /> <has_text text="--min-samples-overall 0.01" /> <has_text text="--filter-haplotype-wise" /> <has_text text="--min_maf 0.01" /> @@ -466,18 +464,18 @@ <param name="min_maf" value="0.01" /> <param name="min_mac" value="1"/> <param name="max_obs_het" value="0.8" /> - <!-- since write_random_snp runs in ifinite loop switch to write_single --> + <!-- since write_random_snp runs in infinite loop switch to write_single --> <param name="filter_single_snp" value="--write_single_snp"/> <param name="blacklist" value="populations/blacklist.tsv" ftype="tabular" /> </section> <assert_command> - <has_text text="-r 0.1" /> - <has_text text="-p 2" /> + <has_text text="--min-samples-per-pop 0.1" /> + <has_text text="--min-populations 2" /> <has_text text="--min-samples-overall 0.01" /> <has_text text="--min_maf 0.01" /> <has_text text="--min_mac 1" /> <has_text text="--max_obs_het 0.8" /> - <has_text text="--write_random_snp" /> + <not_has_text text="--write_random_snp" /> <has_text text="-B " /> </assert_command> <output ftype="txt" name="output_log"><assert_contents><has_text text="Populations is done." /></assert_contents></output> |
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| diff -r 6fba323a242d -r 9a44832748c5 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 14:17:47 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 |