Mercurial > repos > florianbegusch > qiime2_suite
comparison qiime2/qiime_phylogeny_align-to-tree-mafft-fasttree.xml @ 14:a0a8d77a991c draft
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author | florianbegusch |
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date | Thu, 03 Sep 2020 09:51:29 +0000 |
parents | f190567fe3f6 |
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13:887cd4ad8e16 | 14:a0a8d77a991c |
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1 <?xml version="1.0" ?> | 1 <?xml version="1.0" ?> |
2 <tool id="qiime_phylogeny_align-to-tree-mafft-fasttree" name="qiime phylogeny align-to-tree-mafft-fasttree" version="2019.7"> | 2 <tool id="qiime_phylogeny_align-to-tree-mafft-fasttree" name="qiime phylogeny align-to-tree-mafft-fasttree" |
3 <description> - Build a phylogenetic tree using fasttree and mafft alignment</description> | 3 version="2020.8"> |
4 <requirements> | 4 <description>Build a phylogenetic tree using fasttree and mafft alignment</description> |
5 <requirement type="package" version="2019.7">qiime2</requirement> | 5 <requirements> |
6 </requirements> | 6 <requirement type="package" version="2020.8">qiime2</requirement> |
7 <command><![CDATA[ | 7 </requirements> |
8 <command><![CDATA[ | |
8 qiime phylogeny align-to-tree-mafft-fasttree | 9 qiime phylogeny align-to-tree-mafft-fasttree |
9 | 10 |
10 --i-sequences=$isequences | 11 --i-sequences=$isequences |
11 | 12 |
12 #set $pnthreads = '${GALAXY_SLOTS:-4}' | 13 #if str($pnthreads) != 'None': |
13 | 14 --p-n-threads=$pnthreads |
14 #if str($pnthreads): | |
15 --p-n-threads="$pnthreads" | |
16 #end if | 15 #end if |
17 | 16 |
17 --p-mask-max-gap-frequency=$pmaskmaxgapfrequency | |
18 | 18 |
19 #if str($pmaskmaxgapfrequency): | 19 --p-mask-min-conservation=$pmaskminconservation |
20 --p-mask-max-gap-frequency=$pmaskmaxgapfrequency | |
21 #end if | |
22 | 20 |
23 #if str($pmaskminconservation): | 21 #if $pparttree: |
24 --p-mask-min-conservation=$pmaskminconservation | 22 --p-parttree |
25 #end if | 23 #end if |
26 | 24 |
27 --o-alignment=oalignment | 25 --o-alignment=oalignment |
26 | |
28 --o-masked-alignment=omaskedalignment | 27 --o-masked-alignment=omaskedalignment |
28 | |
29 --o-tree=otree | 29 --o-tree=otree |
30 | |
30 --o-rooted-tree=orootedtree | 31 --o-rooted-tree=orootedtree |
32 | |
33 #if str($examples) != 'None': | |
34 --examples=$examples | |
35 #end if | |
36 | |
31 ; | 37 ; |
32 cp oalignment.qza $oalignment; | |
33 cp omaskedalignment.qza $omaskedalignment; | |
34 cp otree.qza $otree; | |
35 cp orootedtree.qza $orootedtree | 38 cp orootedtree.qza $orootedtree |
36 ]]></command> | 39 |
37 <inputs> | 40 ]]></command> |
38 <param format="qza,no_unzip.zip" label="--i-sequences: ARTIFACT FeatureData[Sequence] The sequences to be used for creating a fasttree based rooted phylogenetic tree. [required]" name="isequences" optional="False" type="data"/> | 41 <inputs> |
39 <param label="--p-mask-max-gap-frequency: PROPORTION Range(0, 1, inclusive_end=True) The maximum relative frequency of gap characters in a column for the column to be retained. This relative frequency must be a number between 0.0 and 1.0 (inclusive), where 0.0 retains only those columns without gap characters, and 1.0 retains all columns regardless of gap character frequency. This value is used when masking the aligned sequences. [default: 1.0]" name="pmaskmaxgapfrequency" optional="True" type="float" min="0" max="1" exclusive_end="False" value="1.0"/> | 42 <param format="qza,no_unzip.zip" label="--i-sequences: ARTIFACT FeatureData[Sequence] The sequences to be used for creating a fasttree based rooted phylogenetic tree. [required]" name="isequences" optional="False" type="data" /> |
40 <param label="--p-mask-min-conservation: PROPORTION Range(0, 1, inclusive_end=True) The minimum relative frequency of at least one non-gap character in a column for that column to be retained. This relative frequency must be a number between 0.0 and 1.0 (inclusive). For example, if a value of 0.4 is provided, a column will only be retained if it contains at least one character that is present in at least 40% of the sequences. This value is used when masking the aligned sequences. [default: 0.4]" name="pmaskminconservation" optional="True" type="float" min="0" max="1" exclusive_end="False" value="0.4"/> | 43 <param label="--p-n-threads: " name="pnthreads" optional="True" type="select"> |
41 </inputs> | 44 <option selected="True" value="None">Selection is Optional</option> |
42 <outputs> | 45 <option value="Int % Range(1">Int % Range(1</option> |
43 <data format="qza" label="${tool.name} on ${on_string}: alignment.qza" name="oalignment"/> | 46 <option value="None">None</option> |
44 <data format="qza" label="${tool.name} on ${on_string}: maskedalignment.qza" name="omaskedalignment"/> | 47 </param> |
45 <data format="qza" label="${tool.name} on ${on_string}: tree.qza" name="otree"/> | 48 <param exclude_max="False" label="--p-mask-max-gap-frequency: PROPORTION Range(0, 1, inclusive_end=True) The maximum relative frequency of gap characters in a column for the column to be retained. This relative frequency must be a number between 0.0 and 1.0 (inclusive), where 0.0 retains only those columns without gap characters, and 1.0 retains all columns regardless of gap character frequency. This value is used when masking the aligned sequences. [default: 1.0]" max="1" min="0" name="pmaskmaxgapfrequency" optional="True" type="float" value="1.0" /> |
46 <data format="qza" label="${tool.name} on ${on_string}: rootedtree.qza" name="orootedtree"/> | 49 <param exclude_max="False" label="--p-mask-min-conservation: PROPORTION Range(0, 1, inclusive_end=True) The minimum relative frequency of at least one non-gap character in a column for that column to be retained. This relative frequency must be a number between 0.0 and 1.0 (inclusive). For example, if a value of 0.4 is provided, a column will only be retained if it contains at least one character that is present in at least 40% of the sequences. This value is used when masking the aligned sequences. [default: 0.4]" max="1" min="0" name="pmaskminconservation" optional="True" type="float" value="0.4" /> |
47 </outputs> | 50 <param label="--p-parttree: --p-parttree: / --p-no-parttree This flag is required if the number of sequences being aligned are larger than 1000000. Disabled by default. [default: False]" name="pparttree" selected="False" type="boolean" /> |
48 <help><![CDATA[ | 51 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" /> |
52 | |
53 </inputs> | |
54 | |
55 <outputs> | |
56 <data format="qza" label="${tool.name} on ${on_string}: alignment.qza" name="oalignment" /> | |
57 <data format="qza" label="${tool.name} on ${on_string}: maskedalignment.qza" name="omaskedalignment" /> | |
58 <data format="qza" label="${tool.name} on ${on_string}: tree.qza" name="otree" /> | |
59 <data format="qza" label="${tool.name} on ${on_string}: rootedtree.qza" name="orootedtree" /> | |
60 | |
61 </outputs> | |
62 | |
63 <help><![CDATA[ | |
49 Build a phylogenetic tree using fasttree and mafft alignment | 64 Build a phylogenetic tree using fasttree and mafft alignment |
50 ############################################################ | 65 ############################################################### |
51 | 66 |
52 This pipeline will start by creating a sequence alignment using MAFFT, | 67 This pipeline will start by creating a sequence alignment using MAFFT, |
53 after which any alignment columns that are phylogenetically uninformative | 68 after which any alignment columns that are phylogenetically uninformative |
54 or ambiguously aligned will be removed (masked). The resulting masked | 69 or ambiguously aligned will be removed (masked). The resulting masked |
55 alignment will be used to infer a phylogenetic tree and then subsequently | 70 alignment will be used to infer a phylogenetic tree and then subsequently |
61 Parameters | 76 Parameters |
62 ---------- | 77 ---------- |
63 sequences : FeatureData[Sequence] | 78 sequences : FeatureData[Sequence] |
64 The sequences to be used for creating a fasttree based rooted | 79 The sequences to be used for creating a fasttree based rooted |
65 phylogenetic tree. | 80 phylogenetic tree. |
81 n_threads : Int % Range(1, None) | Str % Choices('auto'), optional | |
82 The number of threads. (Use `auto` to automatically use all available | |
83 cores) This value is used when aligning the sequences and creating the | |
84 tree with fasttree. | |
66 mask_max_gap_frequency : Float % Range(0, 1, inclusive_end=True), optional | 85 mask_max_gap_frequency : Float % Range(0, 1, inclusive_end=True), optional |
67 The maximum relative frequency of gap characters in a column for the | 86 The maximum relative frequency of gap characters in a column for the |
68 column to be retained. This relative frequency must be a number between | 87 column to be retained. This relative frequency must be a number between |
69 0.0 and 1.0 (inclusive), where 0.0 retains only those columns without | 88 0.0 and 1.0 (inclusive), where 0.0 retains only those columns without |
70 gap characters, and 1.0 retains all columns regardless of gap | 89 gap characters, and 1.0 retains all columns regardless of gap |
75 column for that column to be retained. This relative frequency must be | 94 column for that column to be retained. This relative frequency must be |
76 a number between 0.0 and 1.0 (inclusive). For example, if a value of | 95 a number between 0.0 and 1.0 (inclusive). For example, if a value of |
77 0.4 is provided, a column will only be retained if it contains at | 96 0.4 is provided, a column will only be retained if it contains at |
78 least one character that is present in at least 40% of the sequences. | 97 least one character that is present in at least 40% of the sequences. |
79 This value is used when masking the aligned sequences. | 98 This value is used when masking the aligned sequences. |
99 parttree : Bool, optional | |
100 This flag is required if the number of sequences being aligned are | |
101 larger than 1000000. Disabled by default. | |
80 | 102 |
81 Returns | 103 Returns |
82 ------- | 104 ------- |
83 alignment : FeatureData[AlignedSequence] | 105 alignment : FeatureData[AlignedSequence] |
84 The aligned sequences. | 106 The aligned sequences. |
86 The masked alignment. | 108 The masked alignment. |
87 tree : Phylogeny[Unrooted] | 109 tree : Phylogeny[Unrooted] |
88 The unrooted phylogenetic tree. | 110 The unrooted phylogenetic tree. |
89 rooted_tree : Phylogeny[Rooted] | 111 rooted_tree : Phylogeny[Rooted] |
90 The rooted phylogenetic tree. | 112 The rooted phylogenetic tree. |
91 ]]></help> | 113 ]]></help> |
92 <macros> | 114 <macros> |
93 <import>qiime_citation.xml</import> | 115 <import>qiime_citation.xml</import> |
94 </macros> | 116 </macros> |
95 <expand macro="qiime_citation"/> | 117 <expand macro="qiime_citation"/> |
96 </tool> | 118 </tool> |