Mercurial > repos > artbio > concatenate_multiple_datasets
changeset 7:55cf9d9defd1 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 75811bd85c9d175d9bc7b2c4fd723adc3a361f0f
| author | artbio |
|---|---|
| date | Tue, 09 Jul 2019 09:52:16 -0400 |
| parents | 4554fa330d3d |
| children | 5b2cc63d7a21 |
| files | catWrapper.xml test-data/1_options.fastq.gz |
| diffstat | 2 files changed, 18 insertions(+), 14 deletions(-) [+] |
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--- a/catWrapper.xml Mon Jun 24 04:02:53 2019 -0400 +++ b/catWrapper.xml Tue Jul 09 09:52:16 2019 -0400 @@ -1,4 +1,4 @@ -<tool id="cat_multi_datasets" name="Concatenate multiple datasets" version="1.4.0"> +<tool id="cat_multi_datasets" name="Concatenate multiple datasets" version="1.4.1"> <description>tail-to-head by specifying how</description> <command><![CDATA[ #if $headers == 0: @@ -11,11 +11,15 @@ #if $dataset_names == "No": #for $file in $global_condition.inputs printf "${file.element_identifier}..." && - #if $file.ext[-2:] == "gz" and $headers != 0: - gzip -dc '$file' | $concat_command | gzip -c >> '$out_file1' && - #else: + #if $file.ext: + #if $file.ext[-2:] == "gz" and $headers != 0: + gzip -dc '$file' | $concat_command | gzip -c >> '$out_file1' && + #else: + $concat_command '$file' >> '$out_file1' && + #end if + #else: $concat_command '$file' >> '$out_file1' && - #end if + #end if printf "Done\n" && #end for sleep 1 @@ -399,18 +403,18 @@ <param name="collection_cat_type" value="two_collections"/> <param name="input_1"> <collection type="list"> - <element name="1_f.fastq" value="1_f.fastq.gz"/> + <element name="1_f.fastq.gz" value="1_f.fastq.gz"/> </collection> </param> <param name="input_2"> <collection type="list"> - <element name="1_r.fastq" value="1_r.fastq.gz"/> + <element name="1_r.fastq.gz" value="1_r.fastq.gz"/> </collection> </param> <param name="dataset_names" value="Yes" /> <param name="headers" value="4" /> <output_collection name="list_output" type="list" count="1" > - <element name="1_f.fastq_1_r.fastq" file="1_options.fastq.gz" decompress="True"/> + <element name="1_f.fastq.gz_1_r.fastq.gz" file="1_options.fastq.gz" decompress="True"/> </output_collection> </test> <test> <!-- Test nested collections concatenation --> @@ -443,8 +447,8 @@ <collection type="list:list"> <element name="1"> <collection type="list"> - <element name="1_f.fastq" value="1_f.fastq.gz" ftype="fastq.gz"/> - <element name="1_r.fastq" value="1_r.fastq.gz" ftype="fastq.gz"/> + <element name="1_f.fastq.gz" value="1_f.fastq.gz" ftype="fastq.gz"/> + <element name="1_r.fastq.gz" value="1_r.fastq.gz" ftype="fastq.gz"/> </collection> </element> </collection> @@ -460,11 +464,11 @@ .. class:: warningmark -**WARNING:** This tool does not check if the datasets being concatenated are in the same format. +**WARNINGS:** -**WARNING:** When concatenating 2 collections make sure the first collection is the one with the most items. - -**WARNING:** This tool can't handle nested collection deeper than list:list. +- This tool does not check if the datasets being concatenated are in the same format. +- When concatenating 2 collections make sure the first collection is the one with the most items. +- This tool can't handle nested collection deeper than list:list. -----