Mercurial > repos > artbio > concatenate_multiple_datasets
diff catWrapper.xml @ 0:6f54dc6b37da draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
author | artbio |
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date | Sun, 11 Mar 2018 18:19:40 -0400 |
parents | |
children | 3a4694d4354f |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/catWrapper.xml Sun Mar 11 18:19:40 2018 -0400 @@ -0,0 +1,89 @@ +<tool id="cat_multi_datasets" name="Concatenate multiple datasets" version="0.3"> + <description>tail-to-head</description> + <command><![CDATA[ + #if $headers == "No": + cat + #for $file in $input + "$file" + #end for + > "$out_file1" + #else: + #for $file in $input + printf "# ${file.element_identifier}\n" >> "$out_file1" && + cat "$file" >> "$out_file1" && + #end for + sleep 1 + #end if + ]]> + </command> + <inputs> + <param name="headers" type="select" label="include dataset names"> + <option value="No" selected="true">No</option> + <option value="Yes">Yes</option> + </param> + <param name="input" type="data" label="Concatenate Dataset" multiple="True"/> + </inputs> + <outputs> + <data name="out_file1" format_source="input" metadata_source="input"/> + </outputs> + <tests> + <test> + <param name="headers" value="No" /> + <param name="input" value="1.bed,2.bed"/> + <output name="out_file1" file="cat_wrapper_out1.bed"/> + </test> + <test> + <param name="headers" value="Yes" /> + <param name="input" value="1.bed,2.bed"/> + <output name="out_file1" file="cat_wrapper_out2.bed"/> + </test> + + </tests> + <help> + +.. class:: warningmark + +**WARNING:** This tool does not check if the datasets being concatenated are in the same format. + +----- + +**What it does** + +Concatenates datasets + +----- + +**Example** + +Concatenating Dataset:: + + chrX 151087187 151087355 A 0 - + chrX 151572400 151572481 B 0 + + +with Dataset1:: + + chr1 151242630 151242955 X 0 + + chr1 151271715 151271999 Y 0 + + chr1 151278832 151279227 Z 0 - + +and with Dataset2:: + + chr2 100000030 200000955 P 0 + + chr2 100000015 200000999 Q 0 + + +will result in the following:: + + chrX 151087187 151087355 A 0 - + chrX 151572400 151572481 B 0 + + chr1 151242630 151242955 X 0 + + chr1 151271715 151271999 Y 0 + + chr1 151278832 151279227 Z 0 - + chr2 100000030 200000955 P 0 + + chr2 100000015 200000999 Q 0 + + +----- + +Adapted from galaxy's catWrapper.xml to allow multiple input files. + + </help> +</tool>