Mercurial > repos > iuc > trinity_align_and_estimate_abundance
diff align_and_estimate_abundance.xml @ 16:893655fa55f9 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
| author | iuc |
|---|---|
| date | Fri, 19 Mar 2021 21:48:30 +0000 |
| parents | 56162e446004 |
| children | 6c20d62180af |
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--- a/align_and_estimate_abundance.xml Tue Feb 11 12:18:36 2020 -0500 +++ b/align_and_estimate_abundance.xml Fri Mar 19 21:48:30 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="trinity_align_and_estimate_abundance" name="Align reads and estimate abundance" version="@WRAPPER_VERSION@"> +<tool id="trinity_align_and_estimate_abundance" name="Align reads and estimate abundance" version="@WRAPPER_VERSION@+galaxy1"> <description>on a de novo assembly of RNA-Seq data</description> <macros> <import>macros.xml</import> @@ -20,15 +20,20 @@ #if $inputs.left_input.is_of_type('fasta'): ln -s '$inputs.left_input' paired_left.fa && ln -s '$inputs.right_input' paired_right.fa - #else: + #else if $inputs.left_input.is_of_type('fastqsanger'): ln -s '$inputs.left_input' paired_left.fq && ln -s '$inputs.right_input' paired_right.fq + #else: + ln -s '$inputs.left_input' paired_left.fq.gz && + ln -s '$inputs.right_input' paired_right.fq.gz #end if #else: #if $inputs.input.is_of_type('fasta'): ln -s '$inputs.input' single.fa + #else if $inputs.input.is_of_type('fastqsanger'): + ln -s '$inputs.input' single.fq #else: - ln -s '$inputs.input' single.fq + ln -s '$inputs.input' single.fq.gz #end if #end if @@ -47,8 +52,10 @@ #if $inputs.left_input.is_of_type('fasta'): --left paired_left.fa --right paired_right.fa --seqType fa + #else if $inputs.left_input.is_of_type('fastqsanger'): + --left paired_left.fq --right paired_right.fq --seqType fq #else: - --left paired_left.fq --right paired_right.fq --seqType fq + --left paired_left.fq.gz --right paired_right.fq.gz --seqType fq #end if #if $inputs.strand.is_strand_specific: @@ -60,8 +67,10 @@ #else: #if $inputs.input.is_of_type('fasta'): --single single.fa --seqType fa + #else if $inputs.input.is_of_type('fastqsanger'): + --single single.fq --seqType fq #else: - --single single.fq --seqType fq + --single single.fq.gz --seqType fq #end if #if $inputs.strand.is_strand_specific: @@ -87,8 +96,8 @@ <option value="single">Single</option> </param> <when value="paired"> - <param format="fasta,fastqsanger" name="left_input" argument="--left" type="data" label="Left/Forward strand reads" help=""/> - <param format="fasta,fastqsanger" name="right_input" argument="--right" type="data" label="Right/Reverse strand reads" help=""/> + <param format="fasta,fastqsanger,fastqsanger.gz" name="left_input" argument="--left" type="data" label="Left/Forward strand reads" help=""/> + <param format="fasta,fastqsanger,fastqsanger.gz" name="right_input" argument="--right" type="data" label="Right/Reverse strand reads" help=""/> <conditional name="strand"> <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/> <when value="false"> @@ -103,7 +112,7 @@ <param name="paired_fragment_length" argument="--max_ins_size" type="integer" value="800" min="1" label="Maximum insert size" help="bowtie -X parameter"/> </when> <when value="single"> - <param format="fasta,fastqsanger" argument="--single" name="input" type="data" label="Single-end reads" help=""/> + <param format="fasta,fastqsanger,fastqsanger.gz" argument="--single" name="input" type="data" label="Single-end reads" help=""/> <conditional name="strand"> <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/> <when value="false"> @@ -177,8 +186,8 @@ <tests> <test> <param name="paired_or_single" value="paired"/> - <param name="left_input" value="reads.left.fq"/> - <param name="right_input" value="reads.right.fq"/> + <param name="left_input" value="reads.left.fq.gz"/> + <param name="right_input" value="reads.right.fq.gz"/> <param name="transcripts" value="raw/Trinity.fasta"/> <param name="gene_to_trans" value="raw/Trinity.map" /> <param name="library_type" value="RF"/>