smagexp: ImportDataFromMatrix.xml annotate

annotate ImportDataFromMatrix.xml @ 33:2d7595c8041d draft

planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit d42088af604c5a01e1ccebba1d59f7a28a976f71

author	sblanck
date	Thu, 21 Jun 2018 10:06:23 -0400
parents	3d867f8a07ef
children	c08b824e40cc

rev	line source
15 c05f899d5dcd planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit da1436252b5db4e90c39c95140558f0f93544160-dirty sblanck parents: 14 diff changeset	1 <tool id="importMatrixData" name="Import custom data" version="1.0.0">
9 328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 8 diff changeset	2
328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 8 diff changeset	3 <description>Quality control and normalization of a custom matrix expression data</description>
328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 8 diff changeset	4
328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 8 diff changeset	5 <requirements>
17 ef7d98f9eb51 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit f981b0fd5431199f51e2db8c680eb3d2d1d741b6 sblanck parents: 16 diff changeset	6 <requirement type="package">bioconductor-biobase</requirement>
ef7d98f9eb51 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit f981b0fd5431199f51e2db8c680eb3d2d1d741b6 sblanck parents: 16 diff changeset	7 <requirement type="package">bioconductor-geoquery</requirement>
ef7d98f9eb51 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit f981b0fd5431199f51e2db8c680eb3d2d1d741b6 sblanck parents: 16 diff changeset	8 <requirement type="package">bioconductor-geometadb</requirement>
ef7d98f9eb51 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit f981b0fd5431199f51e2db8c680eb3d2d1d741b6 sblanck parents: 16 diff changeset	9 <requirement type="package">bioconductor-limma</requirement>
ef7d98f9eb51 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit f981b0fd5431199f51e2db8c680eb3d2d1d741b6 sblanck parents: 16 diff changeset	10 <requirement type="package">bioconductor-biobase</requirement>
ef7d98f9eb51 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit f981b0fd5431199f51e2db8c680eb3d2d1d741b6 sblanck parents: 16 diff changeset	11 <requirement type="package">bioconductor-affy</requirement>
18 3d867f8a07ef planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 840095a764f473452cdef12053ca9b255267237e-dirty sblanck parents: 17 diff changeset	12 <requirement type="package">bioconductor-affyplm</requirement>
17 ef7d98f9eb51 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit f981b0fd5431199f51e2db8c680eb3d2d1d741b6 sblanck parents: 16 diff changeset	13 <requirement type="package">r-jsonlite</requirement>
ef7d98f9eb51 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit f981b0fd5431199f51e2db8c680eb3d2d1d741b6 sblanck parents: 16 diff changeset	14 <requirement type="package">r-dplyr</requirement>
ef7d98f9eb51 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit f981b0fd5431199f51e2db8c680eb3d2d1d741b6 sblanck parents: 16 diff changeset	15 <requirement type="package">r-optparse</requirement>
ef7d98f9eb51 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit f981b0fd5431199f51e2db8c680eb3d2d1d741b6 sblanck parents: 16 diff changeset	16 </requirements>
9 328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 8 diff changeset	17
328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 8 diff changeset	18 <stdio>
328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 8 diff changeset	19 <exit_code range="1:" />
328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 8 diff changeset	20 <regex match="Warning" source="both" level="warning"/>
328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 8 diff changeset	21 </stdio>
328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 8 diff changeset	22
328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 8 diff changeset	23 <command>
328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 8 diff changeset	24 <![CDATA[
328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 8 diff changeset	25 Rscript --vanilla
328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 8 diff changeset	26 ${__tool_directory__}/ImportDataFromMatrix.R
328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 8 diff changeset	27 --input $input
328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 8 diff changeset	28 --normalization $normalization
328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 8 diff changeset	29 --conditions $conditions
328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 8 diff changeset	30 --annotations $annotations
328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 8 diff changeset	31 --rdataoutput $result_export_eset
328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 8 diff changeset	32 --htmloutput $result_html
328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 8 diff changeset	33 --htmloutputpath $result_html.files_path
328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 8 diff changeset	34 --htmltemplate ${__tool_directory__}/ImportDataFromMatrix_tpl.html
328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 8 diff changeset	35 ]]>
328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 8 diff changeset	36 </command>
328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 8 diff changeset	37
328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 8 diff changeset	38 <inputs>
328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 8 diff changeset	39 <param name="input" type="data" format="tabular" label="Input data" help="Input data"/>
328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 8 diff changeset	40 <param name="normalization" type="select" label="Preprocessing/normalization">
328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 8 diff changeset	41 <option value="quantile">quantile normalization + log2</option>
2 93451f832736 Uploaded sblanck parents: diff changeset	42 <option value="log2">log2 only</option>
93451f832736 Uploaded sblanck parents: diff changeset	43 <option value="none">none</option>
9 328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 8 diff changeset	44 </param>
328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 8 diff changeset	45 <param name="conditions" type="data" format="cond" label="Conditions" help="conditions associated with the input file"/>
328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 8 diff changeset	46 <param name="annotations" type="text" label="Annotation GPL code" help="GPL code for annotations"/>
328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 8 diff changeset	47 </inputs>
2 93451f832736 Uploaded sblanck parents: diff changeset	48
9 328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 8 diff changeset	49 <outputs>
328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 8 diff changeset	50 <data format="rdata" name="result_export_eset" label="export normalized expressionSet"/>
328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 8 diff changeset	51 <data format="html" name="result_html" label="QC result"/>
328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 8 diff changeset	52 </outputs>
2 93451f832736 Uploaded sblanck parents: diff changeset	53
9 328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 8 diff changeset	54 <help>
2 93451f832736 Uploaded sblanck parents: diff changeset	55 <![CDATA[
93451f832736 Uploaded sblanck parents: diff changeset	56 What it does
93451f832736 Uploaded sblanck parents: diff changeset	57
93451f832736 Uploaded sblanck parents: diff changeset	58 This tool imports data stored in a tabular text file.
93451f832736 Uploaded sblanck parents: diff changeset	59 Column titles (chip IDs) must match the IDs of the .cond file.
93451f832736 Uploaded sblanck parents: diff changeset	60 GPL annotation code is also required to fetch annotations from GEO.
93451f832736 Uploaded sblanck parents: diff changeset	61
93451f832736 Uploaded sblanck parents: diff changeset	62 Exemple
93451f832736 Uploaded sblanck parents: diff changeset	63
93451f832736 Uploaded sblanck parents: diff changeset	64 Header of input tabular text file
93451f832736 Uploaded sblanck parents: diff changeset	65 ::
93451f832736 Uploaded sblanck parents: diff changeset	66
8 7f74250a083d planemo upload sblanck parents: 2 diff changeset	67
2 93451f832736 Uploaded sblanck parents: diff changeset	68 "" "GSM80460" "GSM80461" "GSM80462" "GSM80463" "GSM80464"
93451f832736 Uploaded sblanck parents: diff changeset	69 "1007_s_at" -0.0513991525066443 0.306845500314283 0.0854246562526777 -0.142417044615852 0.0854246562526777
93451f832736 Uploaded sblanck parents: diff changeset	70 "1053_at" -0.187707155126729 -0.488026018218199 -0.282789700980404 0.160920188181103 0.989865622866287
93451f832736 Uploaded sblanck parents: diff changeset	71 "117_at" 0.814755482809874 -2.15842936260448 -0.125006361067033 -0.256700472111743 0.0114956388378294
93451f832736 Uploaded sblanck parents: diff changeset	72 "121_at" -0.0558912008920451 -0.0649174766813385 0.49467161164755 -0.0892673380970874 0.113700499164728
93451f832736 Uploaded sblanck parents: diff changeset	73 "1294_at" 0.961993677420255 -0.0320936297098533 -0.169744675832317 -0.0969617298870879 -0.181149439104566
93451f832736 Uploaded sblanck parents: diff changeset	74 "1316_at" 0.0454429707611671 0.43616183931445 -0.766111939825723 -0.182786075741673 0.599317793698226
93451f832736 Uploaded sblanck parents: diff changeset	75 "1405_i_at" 2.23450132056221 0.369606070031838 -1.06190243892591 -0.190997225060914 0.595503660502742
93451f832736 Uploaded sblanck parents: diff changeset	76
93451f832736 Uploaded sblanck parents: diff changeset	77
93451f832736 Uploaded sblanck parents: diff changeset	78 The .cond file should look like this
93451f832736 Uploaded sblanck parents: diff changeset	79 ::
93451f832736 Uploaded sblanck parents: diff changeset	80
93451f832736 Uploaded sblanck parents: diff changeset	81 GSM80460 series of 16 tumors GSM80460 OSCE-2T SERIES OF 16 TUMORS
93451f832736 Uploaded sblanck parents: diff changeset	82 GSM80461 series of 16 tumors GSM80461 OSCE-4T Series of 16 Tumors
93451f832736 Uploaded sblanck parents: diff changeset	83 GSM80462 series of 16 tumors GSM80462 OSCE-6T Series of 16 Tumors
93451f832736 Uploaded sblanck parents: diff changeset	84 GSM80476 series of 4 normals GSM80476 OSCE-2N Series of 4 Normals
93451f832736 Uploaded sblanck parents: diff changeset	85 GSM80477 series of 4 normals GSM80477 OSCE-9N Series of 4 Normals
93451f832736 Uploaded sblanck parents: diff changeset	86
93451f832736 Uploaded sblanck parents: diff changeset	87
93451f832736 Uploaded sblanck parents: diff changeset	88 Results
14 e5a94bc69bd6 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit da1436252b5db4e90c39c95140558f0f93544160 sblanck parents: 9 diff changeset	89 - Boxplots and MA plots
2 93451f832736 Uploaded sblanck parents: diff changeset	90 - Rdata object containing the data for further analysis.
93451f832736 Uploaded sblanck parents: diff changeset	91 ]]>
9 328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 8 diff changeset	92 </help>
2 93451f832736 Uploaded sblanck parents: diff changeset	93
93451f832736 Uploaded sblanck parents: diff changeset	94 </tool>

Mercurial > repos > sblanck > smagexp

annotate ImportDataFromMatrix.xml @ 33:2d7595c8041d draft