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comparison qiime2/qiime_longitudinal_first-differences.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-differences" name="qiime longitudinal first-differences" version="2019.7"> 2 <tool id="qiime_longitudinal_first-differences" name="qiime longitudinal first-differences"
3 <description> - Compute first differences or difference from baseline between sequential states</description> 3 version="2020.8">
4 <requirements> 4 <description>Compute first differences or difference 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-differences 9 qiime longitudinal first-differences
9 10
10 --p-state-column="$pstatecolumn" 11 #if str($itable) != 'None':
11 --p-metric="$pmetric" 12 --i-table=$itable
13 #end if
14 # if $input_files_mmetadatafile:
15 # def list_dict_to_string(list_dict):
16 # set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
17 # for d in list_dict[1:]:
18 # set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
19 # end for
20 # return $file_list
21 # end def
22 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
23 # end if
24
25 #if '__ob__' in str($pstatecolumn):
26 #set $pstatecolumn_temp = $pstatecolumn.replace('__ob__', '[')
27 #set $pstatecolumn = $pstatecolumn_temp
28 #end if
29 #if '__cb__' in str($pstatecolumn):
30 #set $pstatecolumn_temp = $pstatecolumn.replace('__cb__', ']')
31 #set $pstatecolumn = $pstatecolumn_temp
32 #end if
33 #if 'X' in str($pstatecolumn):
34 #set $pstatecolumn_temp = $pstatecolumn.replace('X', '\\')
35 #set $pstatecolumn = $pstatecolumn_temp
36 #end if
37 #if '__sq__' in str($pstatecolumn):
38 #set $pstatecolumn_temp = $pstatecolumn.replace('__sq__', "'")
39 #set $pstatecolumn = $pstatecolumn_temp
40 #end if
41 #if '__db__' in str($pstatecolumn):
42 #set $pstatecolumn_temp = $pstatecolumn.replace('__db__', '"')
43 #set $pstatecolumn = $pstatecolumn_temp
44 #end if
45
46 --p-state-column=$pstatecolumn
12 47
13 48
49 #if '__ob__' in str($pindividualidcolumn):
50 #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__ob__', '[')
51 #set $pindividualidcolumn = $pindividualidcolumn_temp
52 #end if
53 #if '__cb__' in str($pindividualidcolumn):
54 #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__cb__', ']')
55 #set $pindividualidcolumn = $pindividualidcolumn_temp
56 #end if
57 #if 'X' in str($pindividualidcolumn):
58 #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('X', '\\')
59 #set $pindividualidcolumn = $pindividualidcolumn_temp
60 #end if
61 #if '__sq__' in str($pindividualidcolumn):
62 #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__sq__', "'")
63 #set $pindividualidcolumn = $pindividualidcolumn_temp
64 #end if
65 #if '__db__' in str($pindividualidcolumn):
66 #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__db__', '"')
67 #set $pindividualidcolumn = $pindividualidcolumn_temp
68 #end if
14 69
15 #if '__pd__' in str($pindividualidcolumn): 70 --p-individual-id-column=$pindividualidcolumn
16 #set $pwhere_temp = $pindividualidcolumn.replace('__pd__', "#")
17 #set $pindividualidcolumn = $pwhere_temp
18 #end if
19 --p-individual-id-column="$pindividualidcolumn"
20 71
21 72
22 73 --p-metric=$pmetric
23 #if str($itable) != 'None':
24 --i-table=$itable
25 #end if
26 74
27 #if str($preplicatehandling) != 'None': 75 #if str($preplicatehandling) != 'None':
28 --p-replicate-handling=$preplicatehandling 76 --p-replicate-handling=$preplicatehandling
29 #end if 77 #end if
30 78
31 #if str($pbaseline): 79 #if str($pbaseline):
32 --p-baseline="$pbaseline" 80 --p-baseline=$pbaseline
81 #end if
82 --o-first-differences=ofirstdifferences
83
84 #if str($examples) != 'None':
85 --examples=$examples
33 #end if 86 #end if
34 87
35
36 #if $input_files_mmetadatafile:
37 #def list_dict_to_string(list_dict):
38 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
39 #for d in list_dict[1:]:
40 #set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
41 #end for
42 #return $file_list
43 #end def
44 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
45 #end if
46
47
48 --o-first-differences=ofirstdifferences
49 ; 88 ;
50 cp ofirstdifferences.qza $ofirstdifferences 89 cp ofirstdifferences.qza $ofirstdifferences
51 ]]></command>
52 <inputs>
53 <param label="--p-state-column: TEXT Metadata column containing state (time) variable information. [required]" name="pstatecolumn" optional="False" type="text"/>
54 <param label="--p-individual-id-column: TEXT Metadata column containing IDs for individual subjects. [required]" name="pindividualidcolumn" optional="False" type="text"/>
55 <param label="--p-metric: TEXT Numerical metadata or artifact column to test. [required]" name="pmetric" optional="False" type="text"/>
56 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[RelativeFrequency] Feature table to optionally use for computing first differences. [optional]" name="itable" optional="True" type="data"/>
57 <param label="--p-replicate-handling: " name="preplicatehandling" optional="True" type="select">
58 <option selected="True" value="None">Selection is Optional</option>
59 <option value="error">error</option>
60 <option value="random">random</option>
61 <option value="drop">drop</option>
62 </param>
63 <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 differences instead of first differences (which are calculated if no value is given for baseline). If a 'baseline' value is provided, sample differences 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"/>
64 90
65 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file [required]"> 91 ]]></command>
66 <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" /> 92 <inputs>
67 </repeat> 93 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[RelativeFrequency] Feature table to optionally use for computing first differences. [optional]" name="itable" optional="False" type="data" />
94 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
95 <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" />
96 </repeat>
97 <param label="--p-state-column: TEXT Metadata column containing state (time) variable information. [required]" name="pstatecolumn" optional="False" type="text" />
98 <param label="--p-individual-id-column: TEXT Metadata column containing IDs for individual subjects. [required]" name="pindividualidcolumn" optional="False" type="text" />
99 <param label="--p-metric: TEXT Numerical metadata or artifact column to test. [required]" name="pmetric" optional="False" type="text" />
100 <param label="--p-replicate-handling: " name="preplicatehandling" optional="True" type="select">
101 <option selected="True" value="None">Selection is Optional</option>
102 <option value="error">error</option>
103 <option value="random">random</option>
104 <option value="drop">drop</option>
105 </param>
106 <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 differences instead of first differences (which are calculated if no value is given for baseline). If a \'baseline\' value is provided, sample differences 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" />
107 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
108
109 </inputs>
68 110
69 </inputs> 111 <outputs>
70 <outputs> 112 <data format="qza" label="${tool.name} on ${on_string}: firstdifferences.qza" name="ofirstdifferences" />
71 <data format="qza" label="${tool.name} on ${on_string}: firstdifferences.qza" name="ofirstdifferences"/> 113
72 </outputs> 114 </outputs>
73 <help><![CDATA[ 115
116 <help><![CDATA[
74 Compute first differences or difference from baseline between sequential states 117 Compute first differences or difference from baseline between sequential states
75 ############################################################################### 118 ###############################################################
119
76 120
77 Calculates first differences in "metric" between sequential states for 121 Calculates first differences in "metric" between sequential states for
78 samples collected from individual subjects sampled repeatedly at two or 122 samples collected from individual subjects sampled repeatedly at two or
79 more states. First differences can be performed on a metadata column 123 more states. First differences can be performed on a metadata column
80 (including artifacts that can be input as metadata) or a feature in a 124 (including artifacts that can be input as metadata) or a feature in a
115 159
116 Returns 160 Returns
117 ------- 161 -------
118 first_differences : SampleData[FirstDifferences] 162 first_differences : SampleData[FirstDifferences]
119 Series of first differences. 163 Series of first differences.
120 ]]></help> 164 ]]></help>
121 <macros> 165 <macros>
122 <import>qiime_citation.xml</import> 166 <import>qiime_citation.xml</import>
123 </macros> 167 </macros>
124 <expand macro="qiime_citation"/> 168 <expand macro="qiime_citation"/>
125 </tool> 169 </tool>