Mercurial > repos > iuc > ivar_trim
changeset 2:cb903c9dc33d draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
| author | iuc |
|---|---|
| date | Wed, 22 Apr 2020 06:05:42 -0400 |
| parents | d37ede8589b2 |
| children | 5d6ed46cc101 |
| files | ivar_trim.xml macros.xml test-data/primer_scheme_bedfiles.loc test-data/sars-cov-2/SARS-CoV-2-ARTICv1.bed test-data/sars-cov-2/sars_cov2_trimmed.bam test-data/sars-cov-2/sars_cov2_untrimmed.bam tool-data/primer_scheme_bedfiles.loc.sample tool_data_table_conf.xml.sample tool_data_table_conf.xml.test |
| diffstat | 9 files changed, 265 insertions(+), 5 deletions(-) [+] |
line wrap: on
line diff
--- a/ivar_trim.xml Sat Apr 04 12:37:43 2020 -0400 +++ b/ivar_trim.xml Wed Apr 22 06:05:42 2020 -0400 @@ -6,7 +6,11 @@ <expand macro="requirements" /> <expand macro="version_command" /> <command detect_errors="exit_code"><![CDATA[ - ln -s '$input_bed' bed.bed && + #if $primer.source == "history" + ln -s '$primer.input_bed' bed.bed && + #else + ln -s '$primer.cached_bed.fields.path' bed.bed && + #end if ln -s '$input_bam' sorted.bam && ivar trim -i sorted.bam @@ -21,7 +25,23 @@ ]]> </command> <inputs> <param name="input_bam" argument="-i" type="data" format="bam" label="Bam file" help="Aligned reads, to trim primers and quality"/> - <param name="input_bed" argument="-b" type="data" format="bed" label="BED file with primer sequences and positions"/> + <conditional name="primer"> + <param label="Source of primer information" name="source" type="select"> + <option value="history" selected="true">History</option> + <option value="cached">Built-in</option> + </param> + <when value="history"> + <param name="input_bed" argument="-b" type="data" format="bed" label="BED file with primer sequences and positions"/> + </when> + <when value="cached"> + <param name="cached_bed" type="select" label="Primer scheme name" help="Select primer scheme bed file from a list"> + <options from_data_table="primer_scheme_bedfiles"> + <filter type="sort_by" column="1" /> + <validator type="no_options" message="No primer schemes are available" /> + </options> + </param> + </when> + </conditional> <param name="min_len" argument="-m" type="integer" min="0" value="30" label="Minimum length of read to retain after trimming"/> <param name="min_qual" argument="-q" type="integer" min="0" value="20" label="Minimum quality threshold for sliding window to pass"/> <param name="window_width" argument="-s" type="integer" min="0" value="4" label="Width of sliding window"/> @@ -40,15 +60,29 @@ </test> <!-- #1: Zika data--> <test> + <conditional name="primer"> + <param name="source" value="history" /> + <param name="input_bed" value="zika/db/zika_primers.bed" /> + </conditional> <param name="input_bam" value="zika/Z52_a.sorted.bam" /> - <param name="input_bed" value="zika/db/zika_primers.bed" /> <output name="output_bam" file="zika/Z52_a.trimmed.sorted.bam" compare="sim_size" delta="100000"/> </test> <test> + <conditional name="primer"> + <param name="source" value="history" /> + <param name="input_bed" value="zika/db/zika_primers.bed" /> + </conditional> <param name="input_bam" value="zika/Z52_b.sorted.bam" /> - <param name="input_bed" value="zika/db/zika_primers.bed" /> <output name="output_bam" file="zika/Z52_b.trimmed.sorted.bam" compare="sim_size" delta="100000"/> </test> + <test> + <conditional name="primer"> + <param name="source" value="cached" /> + <param name="cached_bed" value="SARS-CoV-2-ARTICv1" /> + </conditional> + <param name="input_bam" value="sars-cov-2/sars_cov2_untrimmed.bam" ftype="bam" /> + <output name="output_bam" file="sars-cov-2/sars_cov2_trimmed.bam" /> + </test> </tests> <help><![CDATA[ iVar uses primer positions supplied in a BED file to soft clip primer
--- a/macros.xml Sat Apr 04 12:37:43 2020 -0400 +++ b/macros.xml Wed Apr 22 06:05:42 2020 -0400 @@ -1,5 +1,5 @@ <macros> - <token name="@VERSION@">1.2</token> + <token name="@VERSION@">1.2.1</token> <xml name="requirements"> <requirements> <requirement type="package" version="@VERSION@">ivar</requirement>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/primer_scheme_bedfiles.loc Wed Apr 22 06:05:42 2020 -0400 @@ -0,0 +1,8 @@ +# this is a tab separated file describing the location of primer schemes used for amplicon +# sequencing (e.g. using the ARTIC SARS-CoV-2 protocol) +# +# the columns are: +# value description path +# +# for example +SARS-CoV-2-ARTICv1 SARS-CoV-2-ARTIC v1 ${__HERE__}/sars-cov-2/SARS-CoV-2-ARTICv1.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sars-cov-2/SARS-CoV-2-ARTICv1.bed Wed Apr 22 06:05:42 2020 -0400 @@ -0,0 +1,196 @@ +MN908947.3 30 54 nCoV-2019_1_LEFT 60 + +MN908947.3 385 410 nCoV-2019_1_RIGHT 60 - +MN908947.3 320 342 nCoV-2019_2_LEFT 60 + +MN908947.3 704 726 nCoV-2019_2_RIGHT 60 - +MN908947.3 642 664 nCoV-2019_3_LEFT 60 + +MN908947.3 1004 1028 nCoV-2019_3_RIGHT 60 - +MN908947.3 943 965 nCoV-2019_4_LEFT 60 + +MN908947.3 1312 1337 nCoV-2019_4_RIGHT 60 - +MN908947.3 1242 1264 nCoV-2019_5_LEFT 60 + +MN908947.3 1623 1651 nCoV-2019_5_RIGHT 60 - +MN908947.3 1573 1595 nCoV-2019_6_LEFT 60 + +MN908947.3 1942 1964 nCoV-2019_6_RIGHT 60 - +MN908947.3 1875 1897 nCoV-2019_7_LEFT 60 + +MN908947.3 2247 2269 nCoV-2019_7_RIGHT 60 - +MN908947.3 2181 2205 nCoV-2019_8_LEFT 60 + +MN908947.3 2568 2592 nCoV-2019_8_RIGHT 60 - +MN908947.3 2505 2529 nCoV-2019_9_LEFT 60 + +MN908947.3 2882 2904 nCoV-2019_9_RIGHT 60 - +MN908947.3 2826 2850 nCoV-2019_10_LEFT 60 + +MN908947.3 3183 3210 nCoV-2019_10_RIGHT 60 - +MN908947.3 3144 3166 nCoV-2019_11_LEFT 60 + +MN908947.3 3507 3531 nCoV-2019_11_RIGHT 60 - +MN908947.3 3460 3482 nCoV-2019_12_LEFT 60 + +MN908947.3 3826 3853 nCoV-2019_12_RIGHT 60 - +MN908947.3 3771 3795 nCoV-2019_13_LEFT 60 + +MN908947.3 4142 4164 nCoV-2019_13_RIGHT 60 - +MN908947.3 4054 4077 nCoV-2019_14_LEFT 60 + +MN908947.3 4428 4450 nCoV-2019_14_RIGHT 60 - +MN908947.3 4294 4321 nCoV-2019_15_LEFT 60 + +MN908947.3 4674 4696 nCoV-2019_15_RIGHT 60 - +MN908947.3 4636 4658 nCoV-2019_16_LEFT 60 + +MN908947.3 4995 5017 nCoV-2019_16_RIGHT 60 - +MN908947.3 4939 4966 nCoV-2019_17_LEFT 60 + +MN908947.3 5296 5321 nCoV-2019_17_RIGHT 60 - +MN908947.3 5230 5259 nCoV-2019_18_LEFT 60 + +MN908947.3 5620 5644 nCoV-2019_18_RIGHT 60 - +MN908947.3 5563 5586 nCoV-2019_19_LEFT 60 + +MN908947.3 5932 5957 nCoV-2019_19_RIGHT 60 - +MN908947.3 5867 5894 nCoV-2019_20_LEFT 60 + +MN908947.3 6247 6272 nCoV-2019_20_RIGHT 60 - +MN908947.3 6167 6196 nCoV-2019_21_LEFT 60 + +MN908947.3 6528 6550 nCoV-2019_21_RIGHT 60 - +MN908947.3 6466 6495 nCoV-2019_22_LEFT 60 + +MN908947.3 6846 6873 nCoV-2019_22_RIGHT 60 - +MN908947.3 6718 6745 nCoV-2019_23_LEFT 60 + +MN908947.3 7092 7117 nCoV-2019_23_RIGHT 60 - +MN908947.3 7035 7058 nCoV-2019_24_LEFT 60 + +MN908947.3 7389 7415 nCoV-2019_24_RIGHT 60 - +MN908947.3 7305 7332 nCoV-2019_25_LEFT 60 + +MN908947.3 7671 7694 nCoV-2019_25_RIGHT 60 - +MN908947.3 7626 7651 nCoV-2019_26_LEFT 60 + +MN908947.3 7997 8019 nCoV-2019_26_RIGHT 60 - +MN908947.3 7943 7968 nCoV-2019_27_LEFT 60 + +MN908947.3 8319 8341 nCoV-2019_27_RIGHT 60 - +MN908947.3 8249 8275 nCoV-2019_28_LEFT 60 + +MN908947.3 8635 8661 nCoV-2019_28_RIGHT 60 - +MN908947.3 8595 8619 nCoV-2019_29_LEFT 60 + +MN908947.3 8954 8983 nCoV-2019_29_RIGHT 60 - +MN908947.3 8888 8913 nCoV-2019_30_LEFT 60 + +MN908947.3 9245 9271 nCoV-2019_30_RIGHT 60 - +MN908947.3 9204 9226 nCoV-2019_31_LEFT 60 + +MN908947.3 9557 9585 nCoV-2019_31_RIGHT 60 - +MN908947.3 9477 9502 nCoV-2019_32_LEFT 60 + +MN908947.3 9834 9858 nCoV-2019_32_RIGHT 60 - +MN908947.3 9784 9806 nCoV-2019_33_LEFT 60 + +MN908947.3 10146 10171 nCoV-2019_33_RIGHT 60 - +MN908947.3 10076 10099 nCoV-2019_34_LEFT 60 + +MN908947.3 10437 10459 nCoV-2019_34_RIGHT 60 - +MN908947.3 10362 10384 nCoV-2019_35_LEFT 60 + +MN908947.3 10737 10763 nCoV-2019_35_RIGHT 60 - +MN908947.3 10666 10688 nCoV-2019_36_LEFT 60 + +MN908947.3 11048 11074 nCoV-2019_36_RIGHT 60 - +MN908947.3 10999 11022 nCoV-2019_37_LEFT 60 + +MN908947.3 11372 11394 nCoV-2019_37_RIGHT 60 - +MN908947.3 11306 11331 nCoV-2019_38_LEFT 60 + +MN908947.3 11668 11693 nCoV-2019_38_RIGHT 60 - +MN908947.3 11555 11584 nCoV-2019_39_LEFT 60 + +MN908947.3 11927 11949 nCoV-2019_39_RIGHT 60 - +MN908947.3 11863 11889 nCoV-2019_40_LEFT 60 + +MN908947.3 12234 12256 nCoV-2019_40_RIGHT 60 - +MN908947.3 12110 12133 nCoV-2019_41_LEFT 60 + +MN908947.3 12465 12490 nCoV-2019_41_RIGHT 60 - +MN908947.3 12417 12439 nCoV-2019_42_LEFT 60 + +MN908947.3 12779 12802 nCoV-2019_42_RIGHT 60 - +MN908947.3 12710 12732 nCoV-2019_43_LEFT 60 + +MN908947.3 13074 13096 nCoV-2019_43_RIGHT 60 - +MN908947.3 13005 13027 nCoV-2019_44_LEFT 60 + +MN908947.3 13378 13400 nCoV-2019_44_RIGHT 60 - +MN908947.3 13319 13344 nCoV-2019_45_LEFT 60 + +MN908947.3 13669 13699 nCoV-2019_45_RIGHT 60 - +MN908947.3 13599 13621 nCoV-2019_46_LEFT 60 + +MN908947.3 13962 13984 nCoV-2019_46_RIGHT 60 - +MN908947.3 13918 13946 nCoV-2019_47_LEFT 60 + +MN908947.3 14271 14299 nCoV-2019_47_RIGHT 60 - +MN908947.3 14207 14232 nCoV-2019_48_LEFT 60 + +MN908947.3 14579 14601 nCoV-2019_48_RIGHT 60 - +MN908947.3 14545 14570 nCoV-2019_49_LEFT 60 + +MN908947.3 14898 14926 nCoV-2019_49_RIGHT 60 - +MN908947.3 14865 14895 nCoV-2019_50_LEFT 60 + +MN908947.3 15224 15246 nCoV-2019_50_RIGHT 60 - +MN908947.3 15171 15193 nCoV-2019_51_LEFT 60 + +MN908947.3 15538 15560 nCoV-2019_51_RIGHT 60 - +MN908947.3 15481 15503 nCoV-2019_52_LEFT 60 + +MN908947.3 15861 15886 nCoV-2019_52_RIGHT 60 - +MN908947.3 15827 15851 nCoV-2019_53_LEFT 60 + +MN908947.3 16186 16209 nCoV-2019_53_RIGHT 60 - +MN908947.3 16118 16144 nCoV-2019_54_LEFT 60 + +MN908947.3 16485 16510 nCoV-2019_54_RIGHT 60 - +MN908947.3 16416 16444 nCoV-2019_55_LEFT 60 + +MN908947.3 16804 16833 nCoV-2019_55_RIGHT 60 - +MN908947.3 16748 16770 nCoV-2019_56_LEFT 60 + +MN908947.3 17130 17152 nCoV-2019_56_RIGHT 60 - +MN908947.3 17065 17087 nCoV-2019_57_LEFT 60 + +MN908947.3 17430 17452 nCoV-2019_57_RIGHT 60 - +MN908947.3 17381 17406 nCoV-2019_58_LEFT 60 + +MN908947.3 17738 17761 nCoV-2019_58_RIGHT 60 - +MN908947.3 17674 17697 nCoV-2019_59_LEFT 60 + +MN908947.3 18036 18062 nCoV-2019_59_RIGHT 60 - +MN908947.3 17966 17993 nCoV-2019_60_LEFT 60 + +MN908947.3 18324 18348 nCoV-2019_60_RIGHT 60 - +MN908947.3 18253 18275 nCoV-2019_61_LEFT 60 + +MN908947.3 18650 18672 nCoV-2019_61_RIGHT 60 - +MN908947.3 18596 18618 nCoV-2019_62_LEFT 60 + +MN908947.3 18957 18979 nCoV-2019_62_RIGHT 60 - +MN908947.3 18896 18918 nCoV-2019_63_LEFT 60 + +MN908947.3 19275 19297 nCoV-2019_63_RIGHT 60 - +MN908947.3 19204 19232 nCoV-2019_64_LEFT 60 + +MN908947.3 19591 19616 nCoV-2019_64_RIGHT 60 - +MN908947.3 19548 19570 nCoV-2019_65_LEFT 60 + +MN908947.3 19911 19939 nCoV-2019_65_RIGHT 60 - +MN908947.3 19844 19866 nCoV-2019_66_LEFT 60 + +MN908947.3 20231 20255 nCoV-2019_66_RIGHT 60 - +MN908947.3 20172 20200 nCoV-2019_67_LEFT 60 + +MN908947.3 20542 20572 nCoV-2019_67_RIGHT 60 - +MN908947.3 20472 20496 nCoV-2019_68_LEFT 60 + +MN908947.3 20867 20890 nCoV-2019_68_RIGHT 60 - +MN908947.3 20786 20813 nCoV-2019_69_LEFT 60 + +MN908947.3 21146 21169 nCoV-2019_69_RIGHT 60 - +MN908947.3 21075 21104 nCoV-2019_70_LEFT 60 + +MN908947.3 21427 21455 nCoV-2019_70_RIGHT 60 - +MN908947.3 21357 21386 nCoV-2019_71_LEFT 60 + +MN908947.3 21716 21743 nCoV-2019_71_RIGHT 60 - +MN908947.3 21658 21682 nCoV-2019_72_LEFT 60 + +MN908947.3 22013 22038 nCoV-2019_72_RIGHT 60 - +MN908947.3 21961 21990 nCoV-2019_73_LEFT 60 + +MN908947.3 22324 22346 nCoV-2019_73_RIGHT 60 - +MN908947.3 22262 22290 nCoV-2019_74_LEFT 60 + +MN908947.3 22626 22650 nCoV-2019_74_RIGHT 60 - +MN908947.3 22516 22542 nCoV-2019_75_LEFT 60 + +MN908947.3 22877 22903 nCoV-2019_75_RIGHT 60 - +MN908947.3 22797 22819 nCoV-2019_76_LEFT 60 + +MN908947.3 23192 23214 nCoV-2019_76_RIGHT 60 - +MN908947.3 23122 23144 nCoV-2019_77_LEFT 60 + +MN908947.3 23500 23522 nCoV-2019_77_RIGHT 60 - +MN908947.3 23443 23466 nCoV-2019_78_LEFT 60 + +MN908947.3 23822 23847 nCoV-2019_78_RIGHT 60 - +MN908947.3 23789 23812 nCoV-2019_79_LEFT 60 + +MN908947.3 24145 24169 nCoV-2019_79_RIGHT 60 - +MN908947.3 24078 24100 nCoV-2019_80_LEFT 60 + +MN908947.3 24443 24467 nCoV-2019_80_RIGHT 60 - +MN908947.3 24391 24416 nCoV-2019_81_LEFT 60 + +MN908947.3 24765 24789 nCoV-2019_81_RIGHT 60 - +MN908947.3 24696 24721 nCoV-2019_82_LEFT 60 + +MN908947.3 25052 25076 nCoV-2019_82_RIGHT 60 - +MN908947.3 24978 25003 nCoV-2019_83_LEFT 60 + +MN908947.3 25347 25369 nCoV-2019_83_RIGHT 60 - +MN908947.3 25279 25301 nCoV-2019_84_LEFT 60 + +MN908947.3 25646 25673 nCoV-2019_84_RIGHT 60 - +MN908947.3 25601 25623 nCoV-2019_85_LEFT 60 + +MN908947.3 25969 25994 nCoV-2019_85_RIGHT 60 - +MN908947.3 25902 25924 nCoV-2019_86_LEFT 60 + +MN908947.3 26290 26315 nCoV-2019_86_RIGHT 60 - +MN908947.3 26197 26219 nCoV-2019_87_LEFT 60 + +MN908947.3 26566 26590 nCoV-2019_87_RIGHT 60 - +MN908947.3 26520 26542 nCoV-2019_88_LEFT 60 + +MN908947.3 26890 26913 nCoV-2019_88_RIGHT 60 - +MN908947.3 26835 26857 nCoV-2019_89_LEFT 60 + +MN908947.3 27202 27227 nCoV-2019_89_RIGHT 60 - +MN908947.3 27141 27164 nCoV-2019_90_LEFT 60 + +MN908947.3 27511 27533 nCoV-2019_90_RIGHT 60 - +MN908947.3 27446 27471 nCoV-2019_91_LEFT 60 + +MN908947.3 27825 27854 nCoV-2019_91_RIGHT 60 - +MN908947.3 27784 27808 nCoV-2019_92_LEFT 60 + +MN908947.3 28145 28172 nCoV-2019_92_RIGHT 60 - +MN908947.3 28081 28104 nCoV-2019_93_LEFT 60 + +MN908947.3 28442 28464 nCoV-2019_93_RIGHT 60 - +MN908947.3 28394 28416 nCoV-2019_94_LEFT 60 + +MN908947.3 28756 28779 nCoV-2019_94_RIGHT 60 - +MN908947.3 28677 28699 nCoV-2019_95_LEFT 60 + +MN908947.3 29041 29063 nCoV-2019_95_RIGHT 60 - +MN908947.3 28985 29007 nCoV-2019_96_LEFT 60 + +MN908947.3 29356 29378 nCoV-2019_96_RIGHT 60 - +MN908947.3 29288 29316 nCoV-2019_97_LEFT 60 + +MN908947.3 29665 29693 nCoV-2019_97_RIGHT 60 - +MN908947.3 29486 29510 nCoV-2019_98_LEFT 60 + +MN908947.3 29836 29866 nCoV-2019_98_RIGHT 60 -
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/primer_scheme_bedfiles.loc.sample Wed Apr 22 06:05:42 2020 -0400 @@ -0,0 +1,8 @@ +# this is a tab separated file describing the location of primer schemes used for amplicon +# sequencing (e.g. using the ARTIC SARS-CoV-2 protocol) +# +# the columns are: +# value description path +# +# for example +# SARS-CoV-2-ARTICv1 SARS-CoV-2-ARTIC v1 primers /data/galaxy/tool_data/artic_primers/SARS-CoV-2-ARTICv1.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Wed Apr 22 06:05:42 2020 -0400 @@ -0,0 +1,7 @@ +<tables> + <!-- Locations of primer scheme BED files --> + <table name="primer_scheme_bedfiles" comment_char="#"> + <columns>value, description, path</columns> + <file path="tool-data/primer_scheme_bedfiles.loc" /> + </table> +</tables>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Wed Apr 22 06:05:42 2020 -0400 @@ -0,0 +1,7 @@ +<tables> + <!-- Locations of primer scheme BED files --> + <table name="primer_scheme_bedfiles" comment_char="#"> + <columns>value, description, path</columns> + <file path="${__HERE__}/test-data/primer_scheme_bedfiles.loc" /> + </table> +</tables>