Mercurial > repos > lecorguille > xcms_merge
comparison xcms_merge.xml @ 11:67ab853b89f3 draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
author | lecorguille |
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date | Tue, 03 Apr 2018 11:38:21 -0400 |
parents | 47e953d9da82 |
children | 2c7d3db37974 |
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10:47e953d9da82 | 11:67ab853b89f3 |
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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 |