comparison xcms_merge.xml @ 11:67ab853b89f3 draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
author lecorguille
date Tue, 03 Apr 2018 11:38:21 -0400
parents 47e953d9da82
children 2c7d3db37974
comparison
equal deleted inserted replaced
10:47e953d9da82 11:67ab853b89f3
1 <tool id="xcms_merge" name="xcms findChromPeaks Merger" version="@WRAPPER_VERSION@.0"> 1 <tool id="xcms_merge" name="xcms findChromPeaks Merger" version="@WRAPPER_VERSION@.0">
2 <description>Merge xcms findChromPeaks RData in one to be used by group</description> 2 <description>Merge xcms findChromPeaks RData in one to be used by group</description>
3 3
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 <import>macros_xcms.xml</import>
6 </macros> 7 </macros>
7 8
8 <expand macro="requirements"/> 9 <expand macro="requirements"/>
9 <expand macro="stdio"/> 10 <expand macro="stdio"/>
10 11
11 <command><![CDATA[ 12 <command><![CDATA[
12 @COMMAND_XCMS_SCRIPT@/xcms_merge.r 13 @COMMAND_RSCRIPT@/xcms_merge.r
13 14
14 images 'c("${"\",\"".join(map(str, $images))}")' 15 images 'c("${"\",\"".join(map(str, $images))}")'
15 16
16 #if str($sampleMetadata) != 'None': 17 #if str($sampleMetadata) != 'None':
17 sampleMetadata '$sampleMetadata' 18 sampleMetadata '$sampleMetadata'
19 20
20 @COMMAND_FILE_LOAD@ 21 @COMMAND_FILE_LOAD@
21 ]]></command> 22 ]]></command>
22 23
23 <inputs> 24 <inputs>
24 <param name="images" type="data" format="rdata.xcms.raw,rdata" label="@INPUT_IMAGE_LABEL@" help="@INPUT_IMAGE_HELP@ from multiple findChromPeaks" multiple="true" /> 25 <param name="images" type="data" format="rdata.xcms.findchrompeaks,rdata" label="@INPUT_IMAGE_LABEL@" help="@INPUT_IMAGE_HELP@ from multiple findChromPeaks" multiple="true" />
25 <param name="sampleMetadata" label="Sample metadata file " format="tabular" type="data" optional="true" help="must contain at least one column with the sample id and one column with the sample class"/> 26 <param name="sampleMetadata" label="Sample metadata file " format="tabular" type="data" optional="true" help="must contain at least one column with the sample id and one column with the sample class"/>
26 27
27 <expand macro="input_file_load"/> 28 <expand macro="input_file_load"/>
28 </inputs> 29 </inputs>
29 30
30 <outputs> 31 <outputs>
31 <data name="xsetRData" format="rdata.xcms.raw" label="xset.merged.RData" from_work_dir="merged.RData" /> 32 <data name="xsetRData" format="rdata.xcms.findchrompeaks" label="xset.merged.RData" from_work_dir="merged.RData" />
32 <data name="sampleMetadataOutput" format="tabular" label="xset.merged.sampleMetadata.tsv" from_work_dir="sampleMetadata.tsv"> 33 <data name="sampleMetadataOutput" format="tabular" label="xset.merged.sampleMetadata.tsv" from_work_dir="sampleMetadata.tsv">
33 <filter>not sampleMetadata</filter> 34 <filter>not sampleMetadata</filter>
34 </data> 35 </data>
35 </outputs> 36 </outputs>
36 37
37 <tests> 38 <tests>
38 <!-- DISABLE FOR TRAVIS 39 <!-- DISABLE FOR TRAVIS
39 <test> 40 <test>
40 <param name="images" value="ko15-xset.RData,ko16-xset.RData,wt15-xset.RData,wt16-xset.RData" /> 41 <param name="images" value="ko15-xset.RData,ko16-xset.RData,wt15-xset.RData,wt16-xset.RData" ftype="rdata"/>
41 <expand macro="test_file_load_single"/> 42 <expand macro="test_file_load_single"/>
42 <assert_stdout> 43 <assert_stdout>
43 <has_text text="object with 4 samples" /> 44 <has_text text="object with 4 samples" />
44 <has_text text="Time range: 2506.1-4477.9 seconds (41.8-74.6 minutes)" /> 45 <has_text text="Time range: 2506.1-4477.9 seconds (41.8-74.6 minutes)" />
45 <has_text text="Mass range: 200.1-600 m/z" /> 46 <has_text text="Mass range: 200.1-600 m/z" />
49 </assert_stdout> 50 </assert_stdout>
50 <output name="sampleMetadataOutput" file="noclass.merged.sampleMetadata.tsv" /> 51 <output name="sampleMetadataOutput" file="noclass.merged.sampleMetadata.tsv" />
51 </test> 52 </test>
52 --> 53 -->
53 <test> 54 <test>
54 <param name="images" value="ko15-xset.RData,ko16-xset.RData,wt15-xset.RData,wt16-xset.RData" /> 55 <param name="images" value="ko15-xset.RData,ko16-xset.RData,wt15-xset.RData,wt16-xset.RData" ftype="rdata"/>
55 <expand macro="test_file_load_single"/> 56 <expand macro="test_file_load_single"/>
56 <param name="sampleMetadata" value="sampleMetadata.tab" /> 57 <param name="sampleMetadata" value="sampleMetadata.tab" />
57 <assert_stdout> 58 <assert_stdout>
58 <has_text_matching expression="ko15\s+KO" /> 59 <has_text_matching expression="ko15\s+KO" />
59 <has_text_matching expression="ko16\s+KO" /> 60 <has_text_matching expression="ko16\s+KO" />
66 <has_text text="Peak Groups: 0" /> 67 <has_text text="Peak Groups: 0" />
67 <has_text text="Sample classes: KO, WT" /> 68 <has_text text="Sample classes: KO, WT" />
68 </assert_stdout> 69 </assert_stdout>
69 </test> 70 </test>
70 <!--<test expect_failure="True"> 71 <!--<test expect_failure="True">
71 <param name="images" value="ko15-xset.RData,ko16-xset.RData,wt15-xset.RData,wt16-xset.RData" /> 72 <param name="images" value="ko15-xset.RData,ko16-xset.RData,wt15-xset.RData,wt16-xset.RData" ftype="rdata"/>
72 <param name="sampleMetadata" value="sampleMetadata_missing.tab" /> 73 <param name="sampleMetadata" value="sampleMetadata_missing.tab" />
73 <expand macro="test_file_load_single"/> 74 <expand macro="test_file_load_single"/>
74 <assert_stderr> 75 <assert_stderr>
75 <has_text text="Those samples are missing in your sampleMetadata: ko16" /> 76 <has_text text="Those samples are missing in your sampleMetadata: ko16" />
76 </assert_stderr> 77 </assert_stderr>
99 Workflow position 100 Workflow position
100 ----------------- 101 -----------------
101 102
102 **Upstream tools** 103 **Upstream tools**
103 104
104 ========================= ================= =================== ========== 105 ========================= ================= ============================== ==========
105 Name output file format parameter 106 Name output file format parameter
106 ========================= ================= =================== ========== 107 ========================= ================= ============================== ==========
107 xcms.xcmsSet xset.RData rdata.xcms.raw RData file 108 xcms.xcmsSet xset.RData rdata.xcms.findchrompeaks RData file
108 ------------------------- ----------------- ------------------- ---------- 109 ------------------------- ----------------- ------------------------------ ----------
109 xcms.xcmsSet xset.RData rdata.xcms.raw RData file 110 xcms.xcmsSet xset.RData rdata.xcms.findchrompeaks RData file
110 ------------------------- ----------------- ------------------- ---------- 111 ------------------------- ----------------- ------------------------------ ----------
111 xcms.xcmsSet xset.RData rdata.xcms.raw RData file 112 xcms.xcmsSet xset.RData rdata.xcms.findchrompeaks RData file
112 ------------------------- ----------------- ------------------- ---------- 113 ------------------------- ----------------- ------------------------------ ----------
113 ... ... ... ... 114 ... ... ... ...
114 ========================= ================= =================== ========== 115 ========================= ================= ============================== ==========
115 116
116 117
117 **Downstream tools** 118 **Downstream tools**
118 119
119 +---------------------------+--------------------+-----------------+ 120 =========================== ==================== ============================
120 | Name | Output file | Format | 121 Name Output file Format
121 +===========================+====================+=================+ 122 =========================== ==================== ============================
122 |xcms.group | xset.RData | rdata.xcms.raw | 123 xcms.group xset.RData rdata.xcms.findchrompeaks
123 +---------------------------+--------------------+-----------------+ 124 =========================== ==================== ============================
124 125
125 .. image:: xcms_merge_workflow.png 126 .. image:: xcms_merge_workflow.png
126 127
127 ----------- 128 -----------
128 Input files 129 Input files
129 ----------- 130 -----------
130 131
131 +---------------------------+-----------------------+ 132 =========================== ==================================
132 | Parameter : num + label | Format | 133 Parameter : num + label Format
133 +===========================+=======================+ 134 =========================== ==================================
134 | 1 : RData file | rdata.xcms.raw | 135 1 : RData file rdata.xcms.findchrompeaks
135 +---------------------------+-----------------------+ 136 --------------------------- ----------------------------------
136 | 2 : RData file | rdata.xcms.raw | 137 2 : RData file rdata.xcms.findchrompeaks
137 +---------------------------+-----------------------+ 138 --------------------------- ----------------------------------
138 | N : RData file | rdata.xcms.raw | 139 N : RData file rdata.xcms.findchrompeaks
139 +---------------------------+-----------------------+ 140 --------------------------- ----------------------------------
140 | Optional : sampleMetadata | tsv or csv | 141 Optional : sampleMetadata tsv or csv
141 +---------------------------+-----------------------+ 142 =========================== ==================================
142 143
143 Example of a sampleMetadata: 144 Example of a sampleMetadata:
144 145
145 +---------------------------+------------+ 146 --------------------------- ------------
146 |HU_neg_028 | bio | 147 HU_neg_028 bio
147 +---------------------------+------------+ 148 --------------------------- ------------
148 |HU_neg_034 | bio | 149 HU_neg_034 bio
149 +---------------------------+------------+ 150 --------------------------- ------------
150 |Blanc04 | blank | 151 Blanc04 blank
151 +---------------------------+------------+ 152 --------------------------- ------------
152 |Blanc06 | blank | 153 Blanc06 blank
153 +---------------------------+------------+ 154 --------------------------- ------------
154 |Blanc09 | blank | 155 Blanc09 blank
155 +---------------------------+------------+ 156 --------------------------- ------------
156 157
157 ------------ 158 ------------
158 Output files 159 Output files
159 ------------ 160 ------------
160 161
161 xset.merged.RData: rdata.xcms.raw format 162 xset.merged.RData: rdata.xcms.findchrompeaks format
162 163
163 | Rdata file that is necessary in the next step of the workflow "xcms.group". 164 | Rdata file that is necessary in the next step of the workflow "xcms.group".
164 165
165 --------------------------------------------------- 166 ---------------------------------------------------
166 167