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comparison qiime2/qiime_longitudinal_first-distances.xml @ 14:a0a8d77a991c draft

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author florianbegusch
date Thu, 03 Sep 2020 09:51:29 +0000
parents f190567fe3f6
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13:887cd4ad8e16 14:a0a8d77a991c
1 <?xml version="1.0" ?> 1 <?xml version="1.0" ?>
2 <tool id="qiime_longitudinal_first-distances" name="qiime longitudinal first-distances" version="2019.7"> 2 <tool id="qiime_longitudinal_first-distances" name="qiime longitudinal first-distances"
3 <description> - Compute first distances or distance from baseline between sequential states</description> 3 version="2020.8">
4 <requirements> 4 <description>Compute first distances or distance from baseline between sequential states</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 longitudinal first-distances 9 qiime longitudinal first-distances
9 10
10 --i-distance-matrix=$idistancematrix 11 --i-distance-matrix=$idistancematrix
11 --p-state-column="$pstatecolumn" 12 # if $input_files_mmetadatafile:
12 --p-individual-id-column="$pindividualidcolumn" 13 # def list_dict_to_string(list_dict):
14 # set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
15 # for d in list_dict[1:]:
16 # set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
17 # end for
18 # return $file_list
19 # end def
20 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
21 # end if
22
23 #if '__ob__' in str($pstatecolumn):
24 #set $pstatecolumn_temp = $pstatecolumn.replace('__ob__', '[')
25 #set $pstatecolumn = $pstatecolumn_temp
26 #end if
27 #if '__cb__' in str($pstatecolumn):
28 #set $pstatecolumn_temp = $pstatecolumn.replace('__cb__', ']')
29 #set $pstatecolumn = $pstatecolumn_temp
30 #end if
31 #if 'X' in str($pstatecolumn):
32 #set $pstatecolumn_temp = $pstatecolumn.replace('X', '\\')
33 #set $pstatecolumn = $pstatecolumn_temp
34 #end if
35 #if '__sq__' in str($pstatecolumn):
36 #set $pstatecolumn_temp = $pstatecolumn.replace('__sq__', "'")
37 #set $pstatecolumn = $pstatecolumn_temp
38 #end if
39 #if '__db__' in str($pstatecolumn):
40 #set $pstatecolumn_temp = $pstatecolumn.replace('__db__', '"')
41 #set $pstatecolumn = $pstatecolumn_temp
42 #end if
43
44 --p-state-column=$pstatecolumn
45
46
47 #if '__ob__' in str($pindividualidcolumn):
48 #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__ob__', '[')
49 #set $pindividualidcolumn = $pindividualidcolumn_temp
50 #end if
51 #if '__cb__' in str($pindividualidcolumn):
52 #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__cb__', ']')
53 #set $pindividualidcolumn = $pindividualidcolumn_temp
54 #end if
55 #if 'X' in str($pindividualidcolumn):
56 #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('X', '\\')
57 #set $pindividualidcolumn = $pindividualidcolumn_temp
58 #end if
59 #if '__sq__' in str($pindividualidcolumn):
60 #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__sq__', "'")
61 #set $pindividualidcolumn = $pindividualidcolumn_temp
62 #end if
63 #if '__db__' in str($pindividualidcolumn):
64 #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__db__', '"')
65 #set $pindividualidcolumn = $pindividualidcolumn_temp
66 #end if
67
68 --p-individual-id-column=$pindividualidcolumn
69
13 70
14 #if str($pbaseline): 71 #if str($pbaseline):
15 --p-baseline="$pbaseline" 72 --p-baseline=$pbaseline
73 #end if
74 #if str($preplicatehandling) != 'None':
75 --p-replicate-handling=$preplicatehandling
16 #end if 76 #end if
17 77
18 #if str($preplicatehandling) != 'None': 78 --o-first-distances=ofirstdistances
19 --p-replicate-handling=$preplicatehandling 79
80 #if str($examples) != 'None':
81 --examples=$examples
20 #end if 82 #end if
21 83
22
23 #if $input_files_mmetadatafile:
24 #def list_dict_to_string(list_dict):
25 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
26 #for d in list_dict[1:]:
27 #set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
28 #end for
29 #return $file_list
30 #end def
31 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
32 #end if
33
34
35 --o-first-distances=ofirstdistances
36 ; 84 ;
37 cp ofirstdistances.qza $ofirstdistances 85 cp ofirstdistances.qza $ofirstdistances
38 ]]></command>
39 <inputs>
40 <param format="qza,no_unzip.zip" label="--i-distance-matrix: ARTIFACT DistanceMatrix Matrix of distances between pairs of samples. [required]" name="idistancematrix" optional="False" type="data"/>
41 <param label="--p-state-column: TEXT Metadata column containing state (time) variable information. [required]" name="pstatecolumn" optional="False" type="text"/>
42 <param label="--p-individual-id-column: TEXT Metadata column containing IDs for individual subjects. [required]" name="pindividualidcolumn" optional="False" type="text"/>
43 <param label="--p-baseline: NUMBER A value listed in the state-column metadata column against which all other states should be compared. Toggles calculation of static distances instead of first distances (which are calculated if no value is given for baseline). If a 'baseline' value is provided, sample distances at each state are compared against the baseline state, instead of the previous state. Must be a value listed in the state-column. [optional]" name="pbaseline" optional="True" type="float"/>
44 <param label="--p-replicate-handling: " name="preplicatehandling" optional="True" type="select">
45 <option selected="True" value="None">Selection is Optional</option>
46 <option value="error">error</option>
47 <option value="random">random</option>
48 <option value="drop">drop</option>
49 </param>
50 86
51 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file [required]"> 87 ]]></command>
52 <param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" /> 88 <inputs>
53 </repeat> 89 <param format="qza,no_unzip.zip" label="--i-distance-matrix: ARTIFACT DistanceMatrix Matrix of distances between pairs of samples. [required]" name="idistancematrix" optional="False" type="data" />
90 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
91 <param format="tabular,qza,no_unzip.zip" label="--m-metadata-file: METADATA... (multiple Sample metadata file containing arguments will be individual-id-column. merged) [required]" name="additional_input" optional="False" type="data" />
92 </repeat>
93 <param label="--p-state-column: TEXT Metadata column containing state (time) variable information. [required]" name="pstatecolumn" optional="False" type="text" />
94 <param label="--p-individual-id-column: TEXT Metadata column containing IDs for individual subjects. [required]" name="pindividualidcolumn" optional="False" type="text" />
95 <param label="--p-baseline: NUMBER A value listed in the state-column metadata column against which all other states should be compared. Toggles calculation of static distances instead of first distances (which are calculated if no value is given for baseline). If a \'baseline\' value is provided, sample distances at each state are compared against the baseline state, instead of the previous state. Must be a value listed in the state-column. [optional]" name="pbaseline" optional="False" type="text" />
96 <param label="--p-replicate-handling: " name="preplicatehandling" optional="True" type="select">
97 <option selected="True" value="None">Selection is Optional</option>
98 <option value="error">error</option>
99 <option value="random">random</option>
100 <option value="drop">drop</option>
101 </param>
102 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
103
104 </inputs>
54 105
55 </inputs> 106 <outputs>
56 <outputs> 107 <data format="qza" label="${tool.name} on ${on_string}: firstdistances.qza" name="ofirstdistances" />
57 <data format="qza" label="${tool.name} on ${on_string}: firstdistances.qza" name="ofirstdistances"/> 108
58 </outputs> 109 </outputs>
59 <help><![CDATA[ 110
111 <help><![CDATA[
60 Compute first distances or distance from baseline between sequential states 112 Compute first distances or distance from baseline between sequential states
61 ########################################################################### 113 ###############################################################
62 114
63 Calculates first distances between sequential states for samples collected 115 Calculates first distances between sequential states for samples collected
64 from individual subjects sampled repeatedly at two or more states. This 116 from individual subjects sampled repeatedly at two or more states. This
65 method is similar to the "first differences" method, except that it 117 method is similar to the "first differences" method, except that it
66 requires a distance matrix as input and calculates first differences as 118 requires a distance matrix as input and calculates first differences as
99 151
100 Returns 152 Returns
101 ------- 153 -------
102 first_distances : SampleData[FirstDifferences] 154 first_distances : SampleData[FirstDifferences]
103 Series of first distances. 155 Series of first distances.
104 ]]></help> 156 ]]></help>
105 <macros> 157 <macros>
106 <import>qiime_citation.xml</import> 158 <import>qiime_citation.xml</import>
107 </macros> 159 </macros>
108 <expand macro="qiime_citation"/> 160 <expand macro="qiime_citation"/>
109 </tool> 161 </tool>