concatenate_multiple_datasets: catWrapper.xml annotate

annotate catWrapper.xml @ 2:745090cbbf75 draft default tip

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit aaca5edd2777ff8fdd13055f11ca9912cb580d2f

author	mvdbeek
date	Fri, 11 Mar 2016 06:05:52 -0500
parents	1bf1794dfcf6
children

rev	line source
1 1bf1794dfcf6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda mvdbeek parents: 0 diff changeset	1 <tool id="cat_multiple" name="Concatenate multiple datasets" version="0.2">
0 cf750d0edbd8 Imported from capsule None mvdbeek parents: diff changeset	2 <description>tail-to-head</description>
1 1bf1794dfcf6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda mvdbeek parents: 0 diff changeset	3 <command><![CDATA[
1bf1794dfcf6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda mvdbeek parents: 0 diff changeset	4 cat
0 cf750d0edbd8 Imported from capsule None mvdbeek parents: diff changeset	5 #for $file in $input
1 1bf1794dfcf6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda mvdbeek parents: 0 diff changeset	6 "$file"
0 cf750d0edbd8 Imported from capsule None mvdbeek parents: diff changeset	7 #end for
1 1bf1794dfcf6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda mvdbeek parents: 0 diff changeset	8 > "$out_file1"
1bf1794dfcf6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda mvdbeek parents: 0 diff changeset	9 ]]>
0 cf750d0edbd8 Imported from capsule None mvdbeek parents: diff changeset	10 </command>
cf750d0edbd8 Imported from capsule None mvdbeek parents: diff changeset	11 <inputs>
cf750d0edbd8 Imported from capsule None mvdbeek parents: diff changeset	12 <param name="input" type="data" label="Concatenate Dataset" multiple="True"/>
cf750d0edbd8 Imported from capsule None mvdbeek parents: diff changeset	13 </inputs>
cf750d0edbd8 Imported from capsule None mvdbeek parents: diff changeset	14 <outputs>
cf750d0edbd8 Imported from capsule None mvdbeek parents: diff changeset	15 <data name="out_file1" format_source="input" metadata_source="input"/>
cf750d0edbd8 Imported from capsule None mvdbeek parents: diff changeset	16 </outputs>
cf750d0edbd8 Imported from capsule None mvdbeek parents: diff changeset	17 <tests>
cf750d0edbd8 Imported from capsule None mvdbeek parents: diff changeset	18 <test>
cf750d0edbd8 Imported from capsule None mvdbeek parents: diff changeset	19 <param name="input" value="1.bed,2.bed"/>
cf750d0edbd8 Imported from capsule None mvdbeek parents: diff changeset	20 <output name="out_file1" file="cat_wrapper_out1.bed"/>
cf750d0edbd8 Imported from capsule None mvdbeek parents: diff changeset	21 </test>
cf750d0edbd8 Imported from capsule None mvdbeek parents: diff changeset	22 </tests>
cf750d0edbd8 Imported from capsule None mvdbeek parents: diff changeset	23 <help>
cf750d0edbd8 Imported from capsule None mvdbeek parents: diff changeset	24
2 745090cbbf75 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit aaca5edd2777ff8fdd13055f11ca9912cb580d2f mvdbeek parents: 1 diff changeset	25 .. class:: warningmark
0 cf750d0edbd8 Imported from capsule None mvdbeek parents: diff changeset	26
2 745090cbbf75 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit aaca5edd2777ff8fdd13055f11ca9912cb580d2f mvdbeek parents: 1 diff changeset	27 WARNING: Be careful not to concatenate datasets of different kinds (e.g., sequences with intervals). This tool does not check if the datasets being concatenated are in the same format.
0 cf750d0edbd8 Imported from capsule None mvdbeek parents: diff changeset	28
2 745090cbbf75 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit aaca5edd2777ff8fdd13055f11ca9912cb580d2f mvdbeek parents: 1 diff changeset	29 -----
0 cf750d0edbd8 Imported from capsule None mvdbeek parents: diff changeset	30
2 745090cbbf75 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit aaca5edd2777ff8fdd13055f11ca9912cb580d2f mvdbeek parents: 1 diff changeset	31 What it does
0 cf750d0edbd8 Imported from capsule None mvdbeek parents: diff changeset	32
2 745090cbbf75 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit aaca5edd2777ff8fdd13055f11ca9912cb580d2f mvdbeek parents: 1 diff changeset	33 Concatenates datasets
0 cf750d0edbd8 Imported from capsule None mvdbeek parents: diff changeset	34
2 745090cbbf75 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit aaca5edd2777ff8fdd13055f11ca9912cb580d2f mvdbeek parents: 1 diff changeset	35 -----
0 cf750d0edbd8 Imported from capsule None mvdbeek parents: diff changeset	36
2 745090cbbf75 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit aaca5edd2777ff8fdd13055f11ca9912cb580d2f mvdbeek parents: 1 diff changeset	37 Example
0 cf750d0edbd8 Imported from capsule None mvdbeek parents: diff changeset	38
2 745090cbbf75 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit aaca5edd2777ff8fdd13055f11ca9912cb580d2f mvdbeek parents: 1 diff changeset	39 Concatenating Dataset::
0 cf750d0edbd8 Imported from capsule None mvdbeek parents: diff changeset	40
2 745090cbbf75 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit aaca5edd2777ff8fdd13055f11ca9912cb580d2f mvdbeek parents: 1 diff changeset	41 chrX 151087187 151087355 A 0 -
745090cbbf75 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit aaca5edd2777ff8fdd13055f11ca9912cb580d2f mvdbeek parents: 1 diff changeset	42 chrX 151572400 151572481 B 0 +
0 cf750d0edbd8 Imported from capsule None mvdbeek parents: diff changeset	43
2 745090cbbf75 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit aaca5edd2777ff8fdd13055f11ca9912cb580d2f mvdbeek parents: 1 diff changeset	44 with Dataset1::
0 cf750d0edbd8 Imported from capsule None mvdbeek parents: diff changeset	45
2 745090cbbf75 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit aaca5edd2777ff8fdd13055f11ca9912cb580d2f mvdbeek parents: 1 diff changeset	46 chr1 151242630 151242955 X 0 +
745090cbbf75 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit aaca5edd2777ff8fdd13055f11ca9912cb580d2f mvdbeek parents: 1 diff changeset	47 chr1 151271715 151271999 Y 0 +
745090cbbf75 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit aaca5edd2777ff8fdd13055f11ca9912cb580d2f mvdbeek parents: 1 diff changeset	48 chr1 151278832 151279227 Z 0 -
0 cf750d0edbd8 Imported from capsule None mvdbeek parents: diff changeset	49
2 745090cbbf75 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit aaca5edd2777ff8fdd13055f11ca9912cb580d2f mvdbeek parents: 1 diff changeset	50 and with Dataset2::
0 cf750d0edbd8 Imported from capsule None mvdbeek parents: diff changeset	51
2 745090cbbf75 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit aaca5edd2777ff8fdd13055f11ca9912cb580d2f mvdbeek parents: 1 diff changeset	52 chr2 100000030 200000955 P 0 +
745090cbbf75 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit aaca5edd2777ff8fdd13055f11ca9912cb580d2f mvdbeek parents: 1 diff changeset	53 chr2 100000015 200000999 Q 0 +
1 1bf1794dfcf6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda mvdbeek parents: 0 diff changeset	54
2 745090cbbf75 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit aaca5edd2777ff8fdd13055f11ca9912cb580d2f mvdbeek parents: 1 diff changeset	55 will result in the following::
0 cf750d0edbd8 Imported from capsule None mvdbeek parents: diff changeset	56
2 745090cbbf75 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit aaca5edd2777ff8fdd13055f11ca9912cb580d2f mvdbeek parents: 1 diff changeset	57 chrX 151087187 151087355 A 0 -
745090cbbf75 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit aaca5edd2777ff8fdd13055f11ca9912cb580d2f mvdbeek parents: 1 diff changeset	58 chrX 151572400 151572481 B 0 +
745090cbbf75 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit aaca5edd2777ff8fdd13055f11ca9912cb580d2f mvdbeek parents: 1 diff changeset	59 chr1 151242630 151242955 X 0 +
745090cbbf75 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit aaca5edd2777ff8fdd13055f11ca9912cb580d2f mvdbeek parents: 1 diff changeset	60 chr1 151271715 151271999 Y 0 +
745090cbbf75 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit aaca5edd2777ff8fdd13055f11ca9912cb580d2f mvdbeek parents: 1 diff changeset	61 chr1 151278832 151279227 Z 0 -
745090cbbf75 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit aaca5edd2777ff8fdd13055f11ca9912cb580d2f mvdbeek parents: 1 diff changeset	62 chr2 100000030 200000955 P 0 +
745090cbbf75 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit aaca5edd2777ff8fdd13055f11ca9912cb580d2f mvdbeek parents: 1 diff changeset	63 chr2 100000015 200000999 Q 0 +
0 cf750d0edbd8 Imported from capsule None mvdbeek parents: diff changeset	64
2 745090cbbf75 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit aaca5edd2777ff8fdd13055f11ca9912cb580d2f mvdbeek parents: 1 diff changeset	65 -----
0 cf750d0edbd8 Imported from capsule None mvdbeek parents: diff changeset	66
2 745090cbbf75 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit aaca5edd2777ff8fdd13055f11ca9912cb580d2f mvdbeek parents: 1 diff changeset	67 Adapted from galaxy's catWrapper.xml to allow multiple input files
745090cbbf75 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit aaca5edd2777ff8fdd13055f11ca9912cb580d2f mvdbeek parents: 1 diff changeset	68
0 cf750d0edbd8 Imported from capsule None mvdbeek parents: diff changeset	69 </help>
cf750d0edbd8 Imported from capsule None mvdbeek parents: diff changeset	70 </tool>

Mercurial > repos > mvdbeek > concatenate_multiple_datasets

annotate catWrapper.xml @ 2:745090cbbf75 draft default tip