diamond: diamond.xml annotate

annotate diamond.xml @ 11:e8ac2b53f262 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 41ed290dd45d61eaf0dffa0cfc61202e03bc1589

author	iuc
date	Thu, 02 Nov 2023 11:14:39 +0000
parents	1e3323a44643
children

rev	line source
10 1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	1 <tool id="bg_diamond" name="Diamond" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="19.01">
0 98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	2 <description>alignment tool for short sequences against a protein database</description>
1 df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	3 <macros>
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	4 <import>macros.xml</import>
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	5 </macros>
11 e8ac2b53f262 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 41ed290dd45d61eaf0dffa0cfc61202e03bc1589 iuc parents: 10 diff changeset	6 <xrefs>
e8ac2b53f262 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 41ed290dd45d61eaf0dffa0cfc61202e03bc1589 iuc parents: 10 diff changeset	7 <xref type="bio.tools">diamond</xref>
e8ac2b53f262 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 41ed290dd45d61eaf0dffa0cfc61202e03bc1589 iuc parents: 10 diff changeset	8 </xrefs>
1 df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	9 <expand macro="requirements" />
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	10 <expand macro="stdio" />
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	11 <expand macro="version_command" />
8 54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	12 <command detect_errors="aggressive">
0 98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	13 <![CDATA[
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	14
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	15 #if $ref_db_source.db_source == "history":
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	16 ln -s $ref_db_source.reference_database ./database.dmnd
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	17 #else:
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	18 ln -s ${ref_db_source.index.fields.db_path} ./database.dmnd
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	19 #end if
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	20
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	21 &&
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	22
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	23 diamond
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	24 $method_cond.method_select
8 54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	25 --quiet
0 98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	26 --threads "\${GALAXY_SLOTS:-12}"
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	27 --db ./database
1 df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	28 --query '$query'
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	29 #if $method_cond.method_select == "blastx"
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	30 --query-gencode '$method_cond.query_gencode'
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	31 --strand '$method_cond.query_strand'
8 54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	32 --min-orf $method_cond.min_orf
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	33 #if $method_cond.frameshift_cond.frameshift_select == 'yes'
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	34 --frameshift $method_cond.frameshift_cond.frameshift
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	35 $method_cond.frameshift_cond.range_culling
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	36 #end if
8 54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	37 #else if $method_cond.method_select == "blastp"
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	38 $method_cond.no_self_hits
3 830516f9521b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 0a893f1ee7f73d24004a43ec1ba6a4cc03fbfab0 bgruening parents: 1 diff changeset	39 #end if
1 df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	40
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	41 @OUTPUT_ARGS@
1 df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	42
10 1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	43 #if $output_section.output.outfmt != '100'
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	44 --compress '0'
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	45 #end if
8 54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	46 $sens_cond.sensitivity
10 1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	47 $iterate
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	48 --algo $algo
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	49 #if $global_ranking
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	50 --global-ranking $global_ranking
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	51 #end if
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	52 #if str($gapopen) != "":
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	53 --gapopen '$gapopen'
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	54 #end if
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	55 #if str($gapextend) != "":
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	56 --gapextend '$gapextend'
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	57 #end if
1 df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	58 --matrix '$matrix'
8 54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	59 --comp-based-stats '$method_cond.comp_based_stats'
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	60 --masking '$masking'
0 98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	61
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	62 @HITFILTER_ARGS@
0 98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	63
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	64 #if str($filter_score.filter_score_select) == 'evalue':
1 df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	65 --evalue '$filter_score.evalue'
0 98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	66 #else:
1 df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	67 --min-score '$filter_score.min_score'
0 98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	68 #end if
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	69
1 df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	70 --id '$id'
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	71 --query-cover '$query_cover'
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	72 --subject-cover '$subject_cover'
8 54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	73 --block-size '$sens_cond.block_size'
10 1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	74 #if $output_section.output_unal
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	75 #if "--un" in $output_section.output_unal
9 f921014aba5a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 828c844036743151594e57cc19811f4c8d9179b3" iuc parents: 8 diff changeset	76 --un '$unalqueries'
f921014aba5a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 828c844036743151594e57cc19811f4c8d9179b3" iuc parents: 8 diff changeset	77 #if $query.ext.startswith("fasta"):
f921014aba5a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 828c844036743151594e57cc19811f4c8d9179b3" iuc parents: 8 diff changeset	78 --unfmt fasta
f921014aba5a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 828c844036743151594e57cc19811f4c8d9179b3" iuc parents: 8 diff changeset	79 #else
f921014aba5a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 828c844036743151594e57cc19811f4c8d9179b3" iuc parents: 8 diff changeset	80 --unfmt fastq
f921014aba5a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 828c844036743151594e57cc19811f4c8d9179b3" iuc parents: 8 diff changeset	81 #end if
f921014aba5a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 828c844036743151594e57cc19811f4c8d9179b3" iuc parents: 8 diff changeset	82 #end if
10 1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	83 #if "--al" in $output_section.output_unal
9 f921014aba5a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 828c844036743151594e57cc19811f4c8d9179b3" iuc parents: 8 diff changeset	84 --al '$alqueries'
f921014aba5a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 828c844036743151594e57cc19811f4c8d9179b3" iuc parents: 8 diff changeset	85 #if $query.ext.startswith("fasta"):
f921014aba5a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 828c844036743151594e57cc19811f4c8d9179b3" iuc parents: 8 diff changeset	86 --alfmt fasta
f921014aba5a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 828c844036743151594e57cc19811f4c8d9179b3" iuc parents: 8 diff changeset	87 #else
f921014aba5a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 828c844036743151594e57cc19811f4c8d9179b3" iuc parents: 8 diff changeset	88 --alfmt fastq
f921014aba5a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 828c844036743151594e57cc19811f4c8d9179b3" iuc parents: 8 diff changeset	89 #end if
f921014aba5a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 828c844036743151594e57cc19811f4c8d9179b3" iuc parents: 8 diff changeset	90 #end if
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	91 #end if
10 1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	92 #if $output_section.max_hsps
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	93 --max-hsps $output_section.max_hsps
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	94 #end if
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	95 #if $tax_cond.tax_select == 'file':
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	96 --taxonlist `cat '$tax_cond.taxonlistfile' \| grep -v "^#" \| grep -v "^$" \| tr "\n" "," \| sed 's/,$//'`
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	97 #else if $tax_cond.tax_select == 'list':
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	98 --taxonlist '$tax_cond.taxonlist'
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	99 #end if
10 1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	100 #if $advanced_section.seed_cut
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	101 --seed-cut $advanced_section.seed_cut
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	102 #end if
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	103 $advanced_section.freq_masking
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	104 --motif-masking $advanced_section.motif_masking
0 98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	105 ]]>
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	106 </command>
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	107 <inputs>
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	108 <conditional name="method_cond">
10 1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	109 <param name="method_select" type="select" label="Alignment mode" help="(blastp/blastx)">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	110 <option value="blastp">Amino acid query sequences (blastp)</option>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	111 <option value="blastx">DNA query sequences (blastx)</option>
3 830516f9521b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 0a893f1ee7f73d24004a43ec1ba6a4cc03fbfab0 bgruening parents: 1 diff changeset	112 </param>
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	113 <when value="blastx">
9 f921014aba5a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 828c844036743151594e57cc19811f4c8d9179b3" iuc parents: 8 diff changeset	114 <param argument="--query-gencode" type="select" label="Genetic code used for translation of query in BLASTX mode" help="">
10 1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	115 <option value="1">Standard Code</option>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	116 <option value="2">Vertebrate Mitochondrial Code</option>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	117 <option value="3">Yeast Mitochondrial Code</option>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	118 <option value="4">Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	119 <option value="5">Invertebrate Mitochondrial Code</option>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	120 <option value="6">Ciliate, Dasycladacean and Hexamita Nuclear Code</option>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	121 <option value="9">Echinoderm and Flatworm Mitochondrial Code</option>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	122 <option value="10">Euplotid Nuclear Code</option>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	123 <option value="11">Bacterial, Archaeal and Plant Plastid Code</option>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	124 <option value="12">Alternative Yeast Nuclear Code</option>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	125 <option value="13">Ascidian Mitochondrial Code</option>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	126 <option value="14">Alternative Flatworm Mitochondrial Code</option>
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	127 <option value="16">Chlorophycean Mitochondrial Code</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	128 <option value="21">Trematode Mitochondrial Code</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	129 <option value="22">Scenedesmus obliquus Mitochondrial Code</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	130 <option value="23">Thraustochytrium Mitochondrial Code</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	131 <option value="24">Pterobranchia Mitochondrial Code</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	132 <option value="25">Candidate Division SR1 and Gracilibacteria Code</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	133 <option value="26">Pachysolen tannophilus Nuclear Code</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	134 </param>
9 f921014aba5a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 828c844036743151594e57cc19811f4c8d9179b3" iuc parents: 8 diff changeset	135 <param argument="--min-orf" type="integer" value="1" label="ignore translated sequences without an open reading frame of at least this length" help="By default this feature is disabled for sequences of length below 30, set to 20 for sequences of length below 100, and set to 40 otherwise. Setting this option to 1 will disable this feature" />
10 1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	136
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	137 <param name="query_strand" argument="--strand" type="select" label="query strands to search" help="">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	138 <option value="both" selected="True">Both</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	139 <option value="plus">Plus</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	140 <option value="minus">Minus</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	141 </param>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	142 <conditional name="frameshift_cond">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	143 <param name="frameshift_select" type="select" label="Allow for frameshifts?" help="">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	144 <option value="yes">yes</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	145 <option value="no" selected="true">no</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	146 </param>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	147 <when value="yes">
9 f921014aba5a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 828c844036743151594e57cc19811f4c8d9179b3" iuc parents: 8 diff changeset	148 <param argument="--range-culling" type="boolean" truevalue="--range-culling" falsevalue="" checked="false" label="restrict hit culling to overlapping query ranges" help="This feature is designed for long query DNA sequences that may span several genes. In these cases, the default of reporting the 25 best overall hits could cause hits to a lower scoring gene to be overshadowed. But just increasing the number of alignments reported will bloat the output size and reduce performance. Using this feature along with -k 25 (default), a hit will only be deleted if at least 50% of its query range is spanned by at least 25 higher or equal scoring hits. Using this feature along with --top 10, a hit will only be deleted if its score is more than 10% lower than that of a higher scoring hit over at least 50% of its query range. The percentage is configurable using --range-cover. Note that this feature is currently only available in frameshift alignment mode"/>
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	149 <param argument="--frameshift" type="integer" value="0" label="frame shift penalty" help="Values around 15 are reasonable for this parameter. Enabling this feature will have the aligner tolerate missing bases in DNA sequences and is most recommended for long, error-prone sequences like MinION reads. In the pairwise output format, frameshifts will be indicated by \ and / for a shift by +1 and -1 nucleotide in the direction of translation respectively." />
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	150 </when>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	151 <when value="no"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	152 </conditional>
8 54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	153
9 f921014aba5a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 828c844036743151594e57cc19811f4c8d9179b3" iuc parents: 8 diff changeset	154 <param argument="--comp-based-stats" type="select" label="Composition based statistics" help="Compositionally biased sequences often cause false positive matches, which are effectively filtered by this algorithm in a way similar to the composition based statistics used by BLAST">
8 54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	155 <option value="0">Disable</option>
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	156 <option value="1" selected="True">Default mode (Hauser, 2016)</option>
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	157 </param>
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	158 </when>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	159 <when value="blastp">
10 1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	160 <param argument="--no-self-hits" type="boolean" truevalue="--no-self-hits" falsevalue="" checked="true"
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	161 label="Suppress reporting of identical self-hits between sequences"
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	162 help="The FASTA sequence identifiers as well as the sequences of query and target need to be identical for a hit to be deleted"/>
8 54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	163
9 f921014aba5a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 828c844036743151594e57cc19811f4c8d9179b3" iuc parents: 8 diff changeset	164 <param argument="--comp-based-stats" type="select" label="Composition based statistics" help="Compositionally biased sequences often cause false positive matches, which are effectively filtered by this algorithm in a way similar to the composition based statistics used by BLAST">
8 54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	165 <option value="0">Disable</option>
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	166 <option value="1" selected="True">Default mode (Hauser, 2016)</option>
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	167 <option value="2">Compositional matrix adjust conditioned on sequence properties, simplified (Yu, 2005)</option>
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	168 <option value="3">Compositional matrix adjust conditioned on sequence properties (Yu, 2005)</option>
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	169 <option value="4">Compositional matrix adjust unconditionally (Yu, 2005)</option>
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	170 </param>
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	171 </when>
3 830516f9521b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 0a893f1ee7f73d24004a43ec1ba6a4cc03fbfab0 bgruening parents: 1 diff changeset	172 </conditional>
1 df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	173 <param argument="--query" type="data" format="fasta,fastq" label="Input query file in FASTA or FASTQ format" />
0 98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	174 <conditional name="ref_db_source">
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	175 <param name="db_source" type="select" label="Will you select a reference database from your history or use a built-in index?" help="Built-ins were indexed using default options">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	176 <option value="indexed">Use a built-in index</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	177 <option value="history">Use one from the history</option>
0 98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	178 </param>
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	179 <when value="indexed">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	180 <param name="index" type="select" label="Select a reference database" help="If your database of interest is not listed, contact your Galaxy admin">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	181 <options from_data_table="diamond_database">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	182 <filter type="sort_by" column="2"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	183 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	184 </options>
1 df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	185 </param>
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	186 </when>
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	187 <when value="history">
8 54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	188 <param name="reference_database" argument="--db" type="data" format="dmnd" label="Select the reference database" />
0 98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	189 </when>
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	190 </conditional>
10 1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	191 <conditional name="tax_cond">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	192 <param name="tax_select" type="select" label="Restrict search taxonomically?" help="Any taxonomic rank can be used, and only reference sequences matching one of the specified taxon ids will be searched against.">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	193 <option value="no" selected="True">No</option>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	194 <option value="list">List of taxids entered manually</option>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	195 <option value="file">List of taxids from single column tabular file</option>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	196 </param>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	197 <when value="no"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	198 <when value="list">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	199 <param name="taxonlist" argument="--taxonlist" type="text" value="" label="Comma separated list of taxon ids" help="">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	200 <validator type="regex" message="Taxonlist needs to be a comma separated list of integers">[0-9,]*</validator>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	201 </param>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	202 </when>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	203 <when value="file">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	204 <param name="taxonlistfile" argument="--taxonlist" type="data" format="tabular" label="Keep alignments within the given percentage range of the top alignment score for a quer" help="" />
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	205 </when>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	206 </conditional>
8 54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	207 <conditional name="sens_cond">
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	208 <param name='sensitivity' type="select" label="Sensitivity Mode" help="Choose one of the sensitivity modes. The default mode is mainly designed for short read alignment, i.e. finding significant matches of >50 bits on 30-40aa fragments. The sensitive mode is a lot more sensitive than the default and generally recommended for aligning longer sequences. The more sensitive mode provides even more sensitivity. More sensitivity may increase computation time.">
10 1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	209 <option value="--fast">Fast (--fast)</option>
8 54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	210 <option value="" selected="True">Default</option>
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	211 <option value="--mid-sensitive">Mid Sensitive (--mid-sensitive)</option>
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	212 <option value="--sensitive">Sensitive (--sensitive)</option>
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	213 <option value="--more-sensitive">More Sensitive (--more-sensitive)</option>
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	214 <option value="--very-sensitive">Very Sensitive (--very-sensitive)</option>
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	215 <option value="--ultra-sensitive">Ultra Sensitive (--ultra-sensitive)</option>
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	216 </param>
10 1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	217 <when value="--fast">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	218 <expand macro="block_size_low_sens"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	219 </when>
8 54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	220 <when value="">
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	221 <expand macro="block_size_low_sens"/>
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	222 </when>
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	223 <when value="--mid-sensitive">
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	224 <expand macro="block_size_low_sens"/>
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	225 </when>
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	226 <when value="--sensitive">
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	227 <expand macro="block_size_low_sens"/>
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	228 </when>
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	229 <when value="--more-sensitive">
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	230 <expand macro="block_size_low_sens"/>
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	231 </when>
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	232 <when value="--very-sensitive">
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	233 <expand macro="block_size_hi_sens"/>
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	234 </when>
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	235 <when value="--ultra-sensitive">
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	236 <expand macro="block_size_hi_sens"/>
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	237 </when>
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	238 </conditional>
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	239 <param argument="--matrix" type="select" label="Scoring matrix" help="In parentheses are the supported values for (gap open)/(gap extend). In brackets are default gap penalties">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	240 <option value="BLOSUM45">BLOSUM45 ((10-13)/3; (12-16)/2; (16-19)/1) [14/2]</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	241 <option value="BLOSUM50">BLOSUM50 ((9-13)/3; (12-16)/2; (15-19)/1) [13/2]</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	242 <option value="BLOSUM62" selected="True">BLOSUM62 ((6-11)/2; (9-13)/1) [11/1]</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	243 <option value="BLOSUM80">BLOSUM80 ((6-9)/2; 13/2; 25/2; (9-11)/1) [10/1]</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	244 <option value="BLOSUM90">BLOSUM90 ((6-9)/2; (9-11)/1) [10/1]</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	245 <option value="PAM250">PAM250 ((11-15)/3; (13-17)/2; (17-21)/1) [14/2]</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	246 <option value="PAM70">PAM70 ((6-8)/2; (9-11)/1) [10/1]</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	247 <option value="PAM30">PAM30 ((5-7)/2; (8-10)/1) [9/1]</option>
3 830516f9521b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 0a893f1ee7f73d24004a43ec1ba6a4cc03fbfab0 bgruening parents: 1 diff changeset	248 </param>
10 1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	249 <param argument="--gapopen" type="integer" optional="True" value="" label="Gap open penalty" help="Leave empty for default (see scoring matrix)" />
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	250 <param argument="--gapextend" type="integer" optional="True" value="" label="Gap extension penalty" help="Leave empty for default (see scoring matrix)" />
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	251 <param argument="--masking" type="select" label="Masking algorithm" help="DIAMOND by default applies the tantan repeat masking algorithm to the query and target sequences as described in (Frith, 2011).
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	252 This masking procedure increases the specificity of alignments and serves to filter out spurious hits. Note that when using --comp-based-stats (2,3,4), tantan masking is disabled by default.">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	253 <option value="0">Disabled</option>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	254 <option value="1" selected="true">Tantan</option>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	255 <option value="seg">SEG</option>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	256 </param>
0 98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	257 <conditional name="filter_score">
1 df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	258 <param name="filter_score_select" type="select" label="Method to filter?" help="(--evalue/--min-score)">
7 62c9df8382c2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit b2d290a8b609ebbc7f4b93716370143c41062ad4" bgruening parents: 6 diff changeset	259 <option value="evalue" selected="True">Maximum e-value to report alignments</option>
1 df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	260 <option value="min-score">Minimum bit score to report alignments</option>
0 98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	261 </param>
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	262 <when value="evalue">
1 df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	263 <param argument="--evalue" type="float" value="0.001" label="Maximum expected value to keep an alignment" />
0 98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	264 </when>
1 df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	265 <when value="min-score">
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	266 <param name="min_score" argument="--min-score" type="integer" value="0" label="Minimum bit score to keep an alignment" help="(--min-score)" />
0 98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	267 </when>
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	268 </conditional>
10 1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	269 <param argument="--iterate" type="boolean" truevalue="--iterate" falsevalue="" checked="false"
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	270 label="Run multiple rounds of searches with increasing sensitivity" help="he query dataset will first be searched at a lower sensitivity setting, only searching those query sequences at
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	271 the target sensitivity that fail to produce a significant alignment at a lower sensitivity." />
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	272 <param argument="--algo" type="select" label="Algorithm for seed search" help="Double-indexed is the main algorithm of the program, designed for large input files but less efficient for small
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	273 query files. Query-indexed and improves performance for small query files. This mode will be automatically triggered based on the input. Contiguous-seed mode and further improves performance
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	274 for small query files. The modes differ slightly in their sensitivity, so results are not guaranteed to be 100% identical for different settings of this option.">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	275 <option value="0">Doble-indexed (0)</option>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	276 <option value="1">Query-indexed (1)</option>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	277 <option value="ctg">Contiguous-seed mode (ctg)</option>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	278 </param>
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	279 <expand macro="hit_filter_macro" />
10 1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	280 <param argument="--global-ranking" type="integer" min="0" value="" optional="true"
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	281 label="Limit on the number of Smith Waterman extensions" help="Target sequences will be ranked according to their ungapped extension scores at seed hits, and gapped extensions will only
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	282 be computed for the best N targets for each query. Note that this option increases memory use." />
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	283 <param argument="--id" type="integer" value="0" label="Minimum identity percentage to report an alignment" help="Report only alignments above the given percentage of sequence identity" />
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	284 <param argument="--query-cover" type="integer" value="0" label="Minimum query cover percentage to report an alignment" help="Report only alignments above the given percentage of query cover" />
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	285 <param argument="--subject-cover" type="integer" value="0" label="Minimum subject cover percentage to report an alignment" help="Report only alignments above the given percentage of subject cover"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	286 <section name="output_section" title="Output options">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	287 <param argument="--max-hsps" type="integer" min="0" optional="true" label="Maximum number of HSPs"
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	288 help="The maximum number of HSPs (High-Scoring Segment Pairs) per target sequence to report for each query. The default policy is to report only the highest-scoring
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	289 HSP for each target, while disregarding alternative, lower-scoring HSPs that are contained in the same target." />
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	290 <expand macro="output_type_macro">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	291 <!-- Taxonomy features are not supported for the DAA format (i.e.
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	292 can't be used in diamond view) -->
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	293 <option value="staxids">unique Subject Taxonomy ID(s), separated by a ';' (in numerical order)</option>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	294 <option value="sskingdoms">Subject super kingdoms</option>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	295 <option value="skingdoms">Subject kingdoms</option>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	296 <option value="sphylums">Subject phylums</option>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	297 </expand>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	298 <param name="output_unal" type="select" optional="true" multiple="true" label="Output aligned/unaligned queries to separate file" help="">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	299 <option value="--un">Output unaligned queries (--un)</option>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	300 <option value="--al">Output alaligned queries (--al)</option>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	301 </param>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	302 </section>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	303 <section name="advanced_section" title="Advanced options" expanded="false">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	304 <param argument="--seed-cut" type="float" min="0" optional="true" label="Set a complexity cutoff for indexed seeds"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	305 <param argument="--freq-masking" type="boolean" truevalue="--freq-masking" falsevalue="" checked="false" label="Enable masking seeds based on frequency" help="This option is incompatible with --sed-cut" />
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	306 <param argument="--motif-masking" type="select" label="Softmask abundant motifs" help="Enable or disable motif masking">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	307 <option value="0">Disabled</option>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	308 <option value="1">Enabled</option>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	309 </param>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	310 </section>
1 df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	311 </inputs>
0 98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	312 <outputs>
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	313 <expand macro="output_macro" />
9 f921014aba5a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 828c844036743151594e57cc19811f4c8d9179b3" iuc parents: 8 diff changeset	314 <data format_source="query" name="unalqueries" label="${tool.name} on ${on_string}: unaligned queries">
10 1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	315 <filter>output_section['output_unal'] and "--un" in output_section['output_unal']</filter>
9 f921014aba5a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 828c844036743151594e57cc19811f4c8d9179b3" iuc parents: 8 diff changeset	316 </data>
f921014aba5a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 828c844036743151594e57cc19811f4c8d9179b3" iuc parents: 8 diff changeset	317 <data format_source="query" name="alqueries" label="${tool.name} on ${on_string}: aligned queries">
10 1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	318 <filter>output_section['output_unal'] and "--un" in output_section['output_unal']</filter>
1 df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	319 </data>
0 98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	320 </outputs>
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	321 <tests>
10 1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	322 <!--Test 01-->
9 f921014aba5a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 828c844036743151594e57cc19811f4c8d9179b3" iuc parents: 8 diff changeset	323 <test expect_num_outputs="3">
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	324 <conditional name="method_cond">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	325 <param name="method_select" value="blastp" />
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	326 </conditional>
0 98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	327 <param name="query" value="protein.fasta" ftype="fasta"/>
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	328 <conditional name="ref_db_source">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	329 <param name="db_source" value="history"/>
8 54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	330 <param name="reference_database" value="db-wtax.dmnd"/>
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	331 </conditional>
10 1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	332 <section name="output_section">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	333 <conditional name="output">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	334 <param name="outfmt" value="6"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	335 <!-- removed ,cigar from test: https://github.com/bbuchfink/diamond/issues/532 -->
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	336 <param name="fields" value="qseqid,sseqid,pident,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore,scovhsp,sskingdoms,skingdoms,sphylums"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	337 <param name="unal" value="true"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	338 </conditional>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	339 </section>
8 54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	340 <conditional name="sens_cond">
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	341 <param name="sensitivity" value=""/>
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	342 </conditional>
1 df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	343 <param name="matrix" value="BLOSUM62"/>
9 f921014aba5a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 828c844036743151594e57cc19811f4c8d9179b3" iuc parents: 8 diff changeset	344 <param name="comp_based_stats" value="1"/>
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	345 <param name="masking" value="1"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	346 <conditional name="hit_filter">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	347 <param name="hit_filter_select" value="max"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	348 <param name="max_target_seqs" value="25" />
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	349 </conditional>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	350 <conditional name="filter_score">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	351 <param name="filter_score_select" value="evalue"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	352 <param name="evalue" value="0.001" />
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	353 </conditional>
1 df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	354 <param name="id" value="0"/>
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	355 <param name="query_cover" value="0"/>
8 54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	356 <conditional name="sens_cond">
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	357 <param name="block_size" value="2"/>
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	358 </conditional>
9 f921014aba5a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 828c844036743151594e57cc19811f4c8d9179b3" iuc parents: 8 diff changeset	359 <param name="output_unal" value="--al,--un"/>
f921014aba5a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 828c844036743151594e57cc19811f4c8d9179b3" iuc parents: 8 diff changeset	360 <output name="unalqueries">
f921014aba5a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 828c844036743151594e57cc19811f4c8d9179b3" iuc parents: 8 diff changeset	361 <assert_contents>
f921014aba5a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 828c844036743151594e57cc19811f4c8d9179b3" iuc parents: 8 diff changeset	362 <has_line line=">shuffled sequence that should go to unaligned"/>
f921014aba5a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 828c844036743151594e57cc19811f4c8d9179b3" iuc parents: 8 diff changeset	363 </assert_contents>
f921014aba5a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 828c844036743151594e57cc19811f4c8d9179b3" iuc parents: 8 diff changeset	364 </output>
f921014aba5a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 828c844036743151594e57cc19811f4c8d9179b3" iuc parents: 8 diff changeset	365 <output name="alqueries">
f921014aba5a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 828c844036743151594e57cc19811f4c8d9179b3" iuc parents: 8 diff changeset	366 <assert_contents>
f921014aba5a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 828c844036743151594e57cc19811f4c8d9179b3" iuc parents: 8 diff changeset	367 <has_line line=">sequence more text"/>
f921014aba5a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 828c844036743151594e57cc19811f4c8d9179b3" iuc parents: 8 diff changeset	368 </assert_contents>
f921014aba5a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 828c844036743151594e57cc19811f4c8d9179b3" iuc parents: 8 diff changeset	369 </output>
1 df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	370 <output name="blast_tabular" file="diamond_results.tabular"/>
0 98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	371 </test>
10 1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	372 <!--Test 02-->
9 f921014aba5a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 828c844036743151594e57cc19811f4c8d9179b3" iuc parents: 8 diff changeset	373 <test expect_num_outputs="1">
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	374 <conditional name="method_cond">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	375 <param name="method_select" value="blastp" />
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	376 </conditional>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	377 <param name="query" value="protein.fasta" ftype="fasta"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	378 <conditional name="ref_db_source">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	379 <param name="db_source" value="history"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	380 <param name="reference_database" value="db-wtax.dmnd"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	381 </conditional>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	382 <conditional name="tax_cond">
8 54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	383 <param name="tax_select" value="list"/>
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	384 <param name="taxonlist" value="2" />
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	385 </conditional>
10 1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	386 <section name="output_section">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	387 <conditional name="output">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	388 <param name="outfmt" value="6"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	389 <param name="fields" value="qseqid,sseqid,pident,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	390 </conditional>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	391 </section>
8 54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	392 <conditional name="sens_cond">
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	393 <param name="sensitivity" value=""/>
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	394 </conditional>
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	395 <param name="matrix" value="BLOSUM62"/>
9 f921014aba5a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 828c844036743151594e57cc19811f4c8d9179b3" iuc parents: 8 diff changeset	396 <param name="comp_based_stats" value="1"/>
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	397 <param name="masking" value="1"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	398 <conditional name="hit_filter">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	399 <param name="hit_filter_select" value="max"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	400 <param name="max_target_seqs" value="25" />
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	401 </conditional>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	402 <conditional name="filter_score">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	403 <param name="filter_score_select" value="evalue"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	404 <param name="evalue" value="0.001" />
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	405 </conditional>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	406 <param name="id" value="0"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	407 <param name="query_cover" value="0"/>
8 54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	408 <conditional name="sens_cond">
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	409 <param name="block_size" value="2"/>
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	410 </conditional>
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	411 <output name="blast_tabular" file="diamond_results.wtax.tabular"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	412 </test>
10 1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	413 <!--Test 03-->
9 f921014aba5a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 828c844036743151594e57cc19811f4c8d9179b3" iuc parents: 8 diff changeset	414 <test expect_num_outputs="1">
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	415 <conditional name="method_cond">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	416 <param name="method_select" value="blastx" />
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	417 <conditional name="frameshift_cond">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	418 <param name="frameshift_select" value="yes"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	419 </conditional>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	420 </conditional>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	421 <param name="query" value="nucleotide.fasta" ftype="fasta"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	422 <conditional name="ref_db_source">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	423 <param name="db_source" value="history"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	424 <param name="reference_database" value="db.dmnd"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	425 </conditional>
10 1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	426 <section name="output_section">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	427 <conditional name="output">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	428 <param name="outfmt" value="0"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	429 </conditional>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	430 </section>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	431 <conditional name="sens_cond">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	432 <param name="sensitivity" value=""/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	433 </conditional>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	434 <param name="matrix" value="BLOSUM62"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	435 <param name="comp_based_stats" value="1"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	436 <param name="masking" value="1"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	437 <conditional name="hit_filter">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	438 <param name="hit_filter_select" value="top"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	439 <param name="top" value="10" />
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	440 </conditional>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	441 <conditional name="filter_score">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	442 <param name="filter_score_select" value="min-score"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	443 <param name="min_score" value="1" />
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	444 </conditional>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	445 <param name="id" value="0"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	446 <param name="query_cover" value="0"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	447 <conditional name="sens_cond">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	448 <param name="block_size" value="2"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	449 </conditional>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	450 <output name="blast_tabular" file="diamond_results.pairwise"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	451 </test>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	452 <!--Test 04-->
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	453 <test expect_num_outputs="1">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	454 <conditional name="method_cond">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	455 <param name="method_select" value="blastp" />
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	456 </conditional>
10 1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	457 <param name="query" value="protein.fasta" ftype="fasta"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	458 <conditional name="ref_db_source">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	459 <param name="db_source" value="history"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	460 <param name="reference_database" value="db-wtax.dmnd"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	461 </conditional>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	462 <section name="output_section">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	463 <conditional name="output">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	464 <param name="outfmt" value="100"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	465 <param name="salltitles" value="false"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	466 <param name="sallseqid" value="false"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	467 </conditional>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	468 </section>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	469 <output name="daa_output" file="diamond_results.daa" compare="sim_size" delta="10"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	470 </test>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	471 <!--Test 05-->
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	472 <test expect_num_outputs="1">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	473 <conditional name="method_cond">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	474 <param name="method_select" value="blastx" />
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	475 <conditional name="frameshift_cond">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	476 <param name="frameshift_select" value="yes"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	477 </conditional>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	478 </conditional>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	479 <param name="query" value="nucleotide.fasta" ftype="fasta"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	480 <conditional name="ref_db_source">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	481 <param name="db_source" value="indexed"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	482 <param name="index" value="testDb"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	483 </conditional>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	484 <section name="output_section">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	485 <conditional name="output">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	486 <param name="outfmt" value="0"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	487 </conditional>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	488 </section>
8 54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	489 <conditional name="sens_cond">
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	490 <param name="sensitivity" value=""/>
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	491 </conditional>
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	492 <param name="matrix" value="BLOSUM62"/>
9 f921014aba5a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 828c844036743151594e57cc19811f4c8d9179b3" iuc parents: 8 diff changeset	493 <param name="comp_based_stats" value="1"/>
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	494 <param name="masking" value="1"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	495 <conditional name="hit_filter">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	496 <param name="hit_filter_select" value="top"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	497 <param name="top" value="10" />
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	498 </conditional>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	499 <conditional name="filter_score">
8 54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	500 <param name="filter_score_select" value="min-score"/>
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	501 <param name="min_score" value="1" />
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	502 </conditional>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	503 <param name="id" value="0"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	504 <param name="query_cover" value="0"/>
8 54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	505 <conditional name="sens_cond">
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	506 <param name="block_size" value="2"/>
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	507 </conditional>
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	508 <output name="blast_tabular" file="diamond_results.pairwise"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	509 </test>
10 1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	510 <!-- Test 06 iterate option-->
9 f921014aba5a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 828c844036743151594e57cc19811f4c8d9179b3" iuc parents: 8 diff changeset	511 <test expect_num_outputs="1">
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	512 <conditional name="method_cond">
10 1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	513 <param name="method_select" value="blastx" />
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	514 </conditional>
10 1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	515 <param name="query" value="nucleotide.fasta" ftype="fasta"/>
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	516 <conditional name="ref_db_source">
10 1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	517 <param name="db_source" value="indexed"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	518 <param name="index" value="testDb"/>
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	519 </conditional>
10 1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	520 <param name="iterate" value="true"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	521 <section name="output_section">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	522 <conditional name="output">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	523 <param name="outfmt" value="6"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	524 <param name="fields" value="qseqid,sseqid,pident,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	525 </conditional>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	526 </section>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	527 <output name="blast_tabular" file="diamond_results_iterate.tabular"/>
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	528 </test>
10 1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	529 <!--Test 07 algo option-->
9 f921014aba5a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 828c844036743151594e57cc19811f4c8d9179b3" iuc parents: 8 diff changeset	530 <test expect_num_outputs="1">
8 54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	531 <conditional name="method_cond">
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	532 <param name="method_select" value="blastx" />
10 1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	533 </conditional>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	534 <param name="query" value="nucleotide.fasta" ftype="fasta"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	535 <conditional name="ref_db_source">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	536 <param name="db_source" value="indexed"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	537 <param name="index" value="testDb"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	538 </conditional>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	539 <param name="algo" value="1"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	540 <section name="output_section">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	541 <conditional name="output">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	542 <param name="outfmt" value="6"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	543 <param name="fields" value="qseqid,sseqid,pident,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore"/>
8 54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	544 </conditional>
10 1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	545 </section>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	546 <output name="blast_tabular" file="diamond_results_algorithm.tabular"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	547 </test>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	548 <!--Test 08 global-ranking option-->
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	549 <test expect_num_outputs="1">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	550 <conditional name="method_cond">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	551 <param name="method_select" value="blastx" />
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	552 </conditional>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	553 <param name="query" value="nucleotide.fasta" ftype="fasta"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	554 <conditional name="ref_db_source">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	555 <param name="db_source" value="indexed"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	556 <param name="index" value="testDb"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	557 </conditional>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	558 <param name="global_ranking" value="10"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	559 <section name="output_section">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	560 <conditional name="output">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	561 <param name="outfmt" value="6"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	562 <param name="fields" value="qseqid,sseqid,pident,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	563 </conditional>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	564 </section>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	565 <output name="blast_tabular" file="diamond_results_global_ranking.tabular"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	566 </test>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	567 <!--Test 09 max-hsps option-->
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	568 <test expect_num_outputs="1">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	569 <conditional name="method_cond">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	570 <param name="method_select" value="blastx" />
8 54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	571 </conditional>
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	572 <param name="query" value="nucleotide.fasta" ftype="fasta"/>
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	573 <conditional name="ref_db_source">
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	574 <param name="db_source" value="indexed"/>
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	575 <param name="index" value="testDb"/>
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	576 </conditional>
10 1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	577 <param name="max_hsps" value="10"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	578 <section name="output_section">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	579 <conditional name="output">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	580 <param name="outfmt" value="6"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	581 <param name="fields" value="qseqid,sseqid,pident,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	582 </conditional>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	583 </section>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	584 <output name="blast_tabular" file="diamond_results_max_hsps.tabular"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	585 </test>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	586 <!--Test 10 seed-cut option-->
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	587 <test expect_num_outputs="1">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	588 <conditional name="method_cond">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	589 <param name="method_select" value="blastx" />
8 54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	590 </conditional>
10 1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	591 <param name="query" value="nucleotide.fasta" ftype="fasta"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	592 <conditional name="ref_db_source">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	593 <param name="db_source" value="indexed"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	594 <param name="index" value="testDb"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	595 </conditional>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	596 <param name="seed_cut" value="100"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	597 <section name="output_section">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	598 <conditional name="output">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	599 <param name="outfmt" value="6"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	600 <param name="fields" value="qseqid,sseqid,pident,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	601 </conditional>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	602 </section>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	603 <output name="blast_tabular" file="diamond_results_seed_cut.tabular"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	604 </test>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	605 <!--Test 11 freq-masking option-->
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	606 <test expect_num_outputs="1">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	607 <conditional name="method_cond">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	608 <param name="method_select" value="blastx" />
8 54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	609 </conditional>
10 1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	610 <param name="query" value="nucleotide.fasta" ftype="fasta"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	611 <conditional name="ref_db_source">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	612 <param name="db_source" value="indexed"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	613 <param name="index" value="testDb"/>
8 54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	614 </conditional>
10 1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	615 <param name="freq_masking" value="true"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	616 <section name="output_section">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	617 <conditional name="output">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	618 <param name="outfmt" value="6"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	619 <param name="fields" value="qseqid,sseqid,pident,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	620 </conditional>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	621 </section>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	622 <output name="blast_tabular" file="diamond_results_freq_masking.tabular"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	623 </test>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	624 <!--Test 12 motif-masking option-->
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	625 <test expect_num_outputs="1">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	626 <conditional name="method_cond">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	627 <param name="method_select" value="blastx" />
8 54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	628 </conditional>
10 1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	629 <param name="query" value="nucleotide.fasta" ftype="fasta"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	630 <conditional name="ref_db_source">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	631 <param name="db_source" value="indexed"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	632 <param name="index" value="testDb"/>
8 54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	633 </conditional>
10 1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	634 <section name="advanced_section">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	635 <param name="motif_masking" value="1"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	636 </section>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	637 <section name="output_section">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	638 <conditional name="output">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	639 <param name="outfmt" value="6"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	640 <param name="fields" value="qseqid,sseqid,pident,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	641 </conditional>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	642 </section>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	643 <output name="blast_tabular" file="diamond_results_motif_masking.tabular"/>
8 54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	644 </test>
0 98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	645 </tests>
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	646 <help>
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	647 <![CDATA[
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	648
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	649 What it does
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	650
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	651 DIAMOND_ is a new alignment tool for aligning short DNA sequencing reads to a protein reference database such as NCBI-NR.
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	652 On Illumina reads of length 100-150bp, in fast mode, DIAMOND is about 20,000 times faster than BLASTX, while reporting
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	653 about 80-90% of all matches that BLASTX finds, with an e-value of at most 1e-5. In sensitive mode, DIAMOND ist about 2,500
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	654 times faster than BLASTX, finding more than 94% of all matches.
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	655
3 830516f9521b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 0a893f1ee7f73d24004a43ec1ba6a4cc03fbfab0 bgruening parents: 1 diff changeset	656 The DIAMOND algorithm is designed for the alignment of large datasets. The algorithm is not efficient for a small number of query sequences or only a single one of them, and speed will be low. BLAST is recommended for small datasets.
1 df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	657
0 98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	658 .. _DIAMOND: http://ab.inf.uni-tuebingen.de/software/diamond/
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	659
1 df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	660 Input
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	661
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	662 Input data is a large protein or nucleotide sequence file.
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	663
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	664
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	665 Output
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	666
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	667 Diamond gives you a tabular output file with 12 columns:
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	668
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	669 Column Description
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	670 1 Query Seq-id (ID of your sequence)
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	671 2 Subject Seq-id (ID of the database hit)
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	672 3 Percentage of identical matches
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	673 4 Alignment length
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	674 5 Number of mismatches
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	675 6 Number of gap openings
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	676 7 Start of alignment in query
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	677 8 End of alignment in query
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	678 9 Start of alignment in subject (database hit)
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	679 10 End of alignment in subject (database hit)
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	680 11 Expectation value (E-value)
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	681 12 Bit score
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	682
0 98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	683
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	684 Supported values for gap open and gap extend parameters depending on the selected scoring matrix.
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	685
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	686 ======== ============================================
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	687 Matrix Supported values for (gap open)/(gap extend)
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	688 ======== ============================================
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	689 BLOSUM45 (10-13)/3; (12-16)/2; (16-19)/1
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	690 BLOSUM50 (9-13)/3; (12-16)/2; (15-19)/1
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	691 BLOSUM62 (6-11)/2; (9-13)/1
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	692 BLOSUM80 (6-9)/2; 13/2; 25/2; (9-11)/1
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	693 BLOSUM90 (6-9)/2; (9-11)/1
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	694 PAM250 (11-15)/3; (13-17)/2; (17-21)/1
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	695 PAM70 (6-8)/2; (9-11)/1
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	696 PAM30 (5-7)/2; (8-10)/1
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	697 ======== ============================================
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	698
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	699
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	700 ]]>
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	701 </help>
1 df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	702 <expand macro="citations" />
0 98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	703 </tool>

Mercurial > repos > bgruening > diamond

annotate diamond.xml @ 11:e8ac2b53f262 draft default tip