Mercurial > repos > iuc > shovill
diff shovill.xml @ 4:d9f6a00b6db7 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit eb617cb0aeeb18710ecb12f5208f4e69b7659dbc"
| author | iuc |
|---|---|
| date | Sun, 25 Aug 2019 05:14:31 -0400 |
| parents | 865119fcb694 |
| children | 8d1af5db538d |
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--- a/shovill.xml Tue Nov 13 10:41:12 2018 -0500 +++ b/shovill.xml Sun Aug 25 05:14:31 2019 -0400 @@ -1,21 +1,31 @@ -<tool id="shovill" name="Shovill" version="1.0.4"> +<tool id="shovill" name="Shovill" version="@TOOL_VERSION@+galaxy0"> <description>Faster SPAdes assembly of Illumina reads</description> + <macros> + <token name="@TOOL_VERSION@">1.0.4</token> + </macros> <requirements> - <requirement type="package" version="1.0.4">shovill</requirement> + <requirement type="package" version="@TOOL_VERSION@">shovill</requirement> </requirements> <version_command>shovill --version</version_command> <command detect_errors="exit_code"><![CDATA[ + #if str($library.lib_type) == "paired" + #set r1_ext = $library.R1.extension + #set r2_ext = $library.R2.extension + ln -s '$library.R1' fastq_r1.'$r1_ext' && + ln -s '$library.R2' fastq_r2.'$r2_ext' && + #else if str($library.lib_type) == "collection" + #set r1_ext = $library.input1.forward.extension + #set r2_ext = $library.input1.reverse.extension + ln -s '$library.input1.forward' fastq_r1.'$r1_ext' && + ln -s '$library.input1.reverse' fastq_r2.'$r2_ext' && + #end if + shovill --outdir 'out' --cpus \${GALAXY_SLOTS:-1} --ram \${SHOVILL_RAM:-4} - #if str($library.lib_type) == "paired" - --R1 '$library.R1' - --R2 '$library.R2' - #else if str($library.lib_type) == "collection" - --R1 '$library.input1.forward' - --R2 '$library.input1.reverse' - #end if + --R1 fastq_r1.'$r1_ext' + --R2 fastq_r2.'$r2_ext' $trim --namefmt '$adv.namefmt' --depth '$adv.depth' @@ -98,7 +108,7 @@ <output name="shovill_std_log" ftype="txt" > <assert_contents> <has_text text="[mash]"/> - <has_text text="[lighter] Processed 24960 reads"/> + <has_text text="[lighter] Processed 1714 reads"/> <has_text text="[FLASH] FLASH v1.2.11 complete!"/> <has_text text="[spades] ======= SPAdes pipeline finished."/> </assert_contents> @@ -125,7 +135,7 @@ <assert_contents> <has_text text="[mash] Writing to"/> <has_text text="[trimmomatic] TrimmomaticPE: Completed successfully"/> - <has_text text="[lighter] Processed 24960 reads:"/> + <has_text text="[lighter] Processed 2000 reads:"/> <has_text text="[FLASH] FLASH v1.2.11 complete!"/> <has_text text="[spades] ======= SPAdes pipeline finished."/> <has_text text="[bwa+samtools-sort] [samclip] Done."/> @@ -147,9 +157,9 @@ <output name="shovill_std_log" ftype="txt" > <assert_contents> <has_text text="[mash]"/> - <has_text text="[lighter] Processed 24960 reads"/> + <has_text text="[lighter] Processed 1714 reads"/> <has_text text="[FLASH] FLASH v1.2.11 complete!"/> - <has_text text="[megahit] --- [STAT]"/> + <has_text_matching expression="\[megahit\] .* ALL DONE"/> </assert_contents> </output> </test> @@ -166,7 +176,7 @@ <output name="shovill_std_log" ftype="txt" > <assert_contents> <has_text text="[mash]"/> - <has_text text="[lighter] Processed 24960 reads"/> + <has_text text="[lighter] Processed 1714 reads"/> <has_text text="[FLASH] FLASH v1.2.11 complete!"/> <has_text text="[skesa] DONE"/> </assert_contents> @@ -185,12 +195,31 @@ <output name="shovill_std_log" ftype="txt" > <assert_contents> <has_text text="[mash]"/> - <has_text text="[lighter] Processed 24960 reads"/> + <has_text text="[lighter] Processed 1714 reads"/> <has_text text="[FLASH] FLASH v1.2.11 complete!"/> <has_text text="[velvetg] Final graph has"/> </assert_contents> </output> </test> + <test> <!-- Test 6: Gzipped input with trimming --> + <param name="lib_type" value="paired" /> + <param name="R1" value="mutant_R1.fastq.gz" ftype="fastqsanger" /> + <param name="R2" value="mutant_R2.fastq.gz" ftype="fastqsanger" /> + <param name="trim" value="true" /> + <output name="contigs" ftype="fasta"> + <assert_contents> + <has_text text=">contig00001"/> + </assert_contents> + </output> + <output name="shovill_std_log" ftype="txt" > + <assert_contents> + <has_text text="[mash]"/> + <has_text text="[lighter] Processed 1714 reads"/> + <has_text text="[FLASH] FLASH v1.2.11 complete!"/> + <has_text text="[spades] ======= SPAdes pipeline finished."/> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[ Synopsis: