Mercurial > repos > iuc > trinity_align_and_estimate_abundance
comparison 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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| 15:56162e446004 | 16:893655fa55f9 |
|---|---|
| 1 <tool id="trinity_align_and_estimate_abundance" name="Align reads and estimate abundance" version="@WRAPPER_VERSION@"> | 1 <tool id="trinity_align_and_estimate_abundance" name="Align reads and estimate abundance" version="@WRAPPER_VERSION@+galaxy1"> |
| 2 <description>on a de novo assembly of RNA-Seq data</description> | 2 <description>on a de novo assembly of RNA-Seq data</description> |
| 3 <macros> | 3 <macros> |
| 4 <import>macros.xml</import> | 4 <import>macros.xml</import> |
| 5 </macros> | 5 </macros> |
| 6 <expand macro="requirements"> | 6 <expand macro="requirements"> |
| 18 | 18 |
| 19 #if $inputs.paired_or_single == "paired": | 19 #if $inputs.paired_or_single == "paired": |
| 20 #if $inputs.left_input.is_of_type('fasta'): | 20 #if $inputs.left_input.is_of_type('fasta'): |
| 21 ln -s '$inputs.left_input' paired_left.fa && | 21 ln -s '$inputs.left_input' paired_left.fa && |
| 22 ln -s '$inputs.right_input' paired_right.fa | 22 ln -s '$inputs.right_input' paired_right.fa |
| 23 #else: | 23 #else if $inputs.left_input.is_of_type('fastqsanger'): |
| 24 ln -s '$inputs.left_input' paired_left.fq && | 24 ln -s '$inputs.left_input' paired_left.fq && |
| 25 ln -s '$inputs.right_input' paired_right.fq | 25 ln -s '$inputs.right_input' paired_right.fq |
| 26 #else: | |
| 27 ln -s '$inputs.left_input' paired_left.fq.gz && | |
| 28 ln -s '$inputs.right_input' paired_right.fq.gz | |
| 26 #end if | 29 #end if |
| 27 #else: | 30 #else: |
| 28 #if $inputs.input.is_of_type('fasta'): | 31 #if $inputs.input.is_of_type('fasta'): |
| 29 ln -s '$inputs.input' single.fa | 32 ln -s '$inputs.input' single.fa |
| 33 #else if $inputs.input.is_of_type('fastqsanger'): | |
| 34 ln -s '$inputs.input' single.fq | |
| 30 #else: | 35 #else: |
| 31 ln -s '$inputs.input' single.fq | 36 ln -s '$inputs.input' single.fq.gz |
| 32 #end if | 37 #end if |
| 33 #end if | 38 #end if |
| 34 | 39 |
| 35 && | 40 && |
| 36 | 41 |
| 45 | 50 |
| 46 #if $inputs.paired_or_single == "paired": | 51 #if $inputs.paired_or_single == "paired": |
| 47 | 52 |
| 48 #if $inputs.left_input.is_of_type('fasta'): | 53 #if $inputs.left_input.is_of_type('fasta'): |
| 49 --left paired_left.fa --right paired_right.fa --seqType fa | 54 --left paired_left.fa --right paired_right.fa --seqType fa |
| 55 #else if $inputs.left_input.is_of_type('fastqsanger'): | |
| 56 --left paired_left.fq --right paired_right.fq --seqType fq | |
| 50 #else: | 57 #else: |
| 51 --left paired_left.fq --right paired_right.fq --seqType fq | 58 --left paired_left.fq.gz --right paired_right.fq.gz --seqType fq |
| 52 #end if | 59 #end if |
| 53 | 60 |
| 54 #if $inputs.strand.is_strand_specific: | 61 #if $inputs.strand.is_strand_specific: |
| 55 --SS_lib_type $inputs.strand.library_type | 62 --SS_lib_type $inputs.strand.library_type |
| 56 #end if | 63 #end if |
| 58 --max_ins_size $inputs.paired_fragment_length | 65 --max_ins_size $inputs.paired_fragment_length |
| 59 | 66 |
| 60 #else: | 67 #else: |
| 61 #if $inputs.input.is_of_type('fasta'): | 68 #if $inputs.input.is_of_type('fasta'): |
| 62 --single single.fa --seqType fa | 69 --single single.fa --seqType fa |
| 70 #else if $inputs.input.is_of_type('fastqsanger'): | |
| 71 --single single.fq --seqType fq | |
| 63 #else: | 72 #else: |
| 64 --single single.fq --seqType fq | 73 --single single.fq.gz --seqType fq |
| 65 #end if | 74 #end if |
| 66 | 75 |
| 67 #if $inputs.strand.is_strand_specific: | 76 #if $inputs.strand.is_strand_specific: |
| 68 --SS_lib_type $inputs.strand.library_type | 77 --SS_lib_type $inputs.strand.library_type |
| 69 #end if | 78 #end if |
| 85 <param name="paired_or_single" type="select" label="Paired or Single-end data?"> | 94 <param name="paired_or_single" type="select" label="Paired or Single-end data?"> |
| 86 <option value="paired">Paired</option> | 95 <option value="paired">Paired</option> |
| 87 <option value="single">Single</option> | 96 <option value="single">Single</option> |
| 88 </param> | 97 </param> |
| 89 <when value="paired"> | 98 <when value="paired"> |
| 90 <param format="fasta,fastqsanger" name="left_input" argument="--left" type="data" label="Left/Forward strand reads" help=""/> | 99 <param format="fasta,fastqsanger,fastqsanger.gz" name="left_input" argument="--left" type="data" label="Left/Forward strand reads" help=""/> |
| 91 <param format="fasta,fastqsanger" name="right_input" argument="--right" type="data" label="Right/Reverse strand reads" help=""/> | 100 <param format="fasta,fastqsanger,fastqsanger.gz" name="right_input" argument="--right" type="data" label="Right/Reverse strand reads" help=""/> |
| 92 <conditional name="strand"> | 101 <conditional name="strand"> |
| 93 <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/> | 102 <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/> |
| 94 <when value="false"> | 103 <when value="false"> |
| 95 </when> | 104 </when> |
| 96 <when value="true"> | 105 <when value="true"> |
| 101 </when> | 110 </when> |
| 102 </conditional> | 111 </conditional> |
| 103 <param name="paired_fragment_length" argument="--max_ins_size" type="integer" value="800" min="1" label="Maximum insert size" help="bowtie -X parameter"/> | 112 <param name="paired_fragment_length" argument="--max_ins_size" type="integer" value="800" min="1" label="Maximum insert size" help="bowtie -X parameter"/> |
| 104 </when> | 113 </when> |
| 105 <when value="single"> | 114 <when value="single"> |
| 106 <param format="fasta,fastqsanger" argument="--single" name="input" type="data" label="Single-end reads" help=""/> | 115 <param format="fasta,fastqsanger,fastqsanger.gz" argument="--single" name="input" type="data" label="Single-end reads" help=""/> |
| 107 <conditional name="strand"> | 116 <conditional name="strand"> |
| 108 <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/> | 117 <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/> |
| 109 <when value="false"> | 118 <when value="false"> |
| 110 </when> | 119 </when> |
| 111 <when value="true"> | 120 <when value="true"> |
| 175 </data> | 184 </data> |
| 176 </outputs> | 185 </outputs> |
| 177 <tests> | 186 <tests> |
| 178 <test> | 187 <test> |
| 179 <param name="paired_or_single" value="paired"/> | 188 <param name="paired_or_single" value="paired"/> |
| 180 <param name="left_input" value="reads.left.fq"/> | 189 <param name="left_input" value="reads.left.fq.gz"/> |
| 181 <param name="right_input" value="reads.right.fq"/> | 190 <param name="right_input" value="reads.right.fq.gz"/> |
| 182 <param name="transcripts" value="raw/Trinity.fasta"/> | 191 <param name="transcripts" value="raw/Trinity.fasta"/> |
| 183 <param name="gene_to_trans" value="raw/Trinity.map" /> | 192 <param name="gene_to_trans" value="raw/Trinity.map" /> |
| 184 <param name="library_type" value="RF"/> | 193 <param name="library_type" value="RF"/> |
| 185 <param name="est_method" value="RSEM"/> | 194 <param name="est_method" value="RSEM"/> |
| 186 <param name="aln_method" value="bowtie"/> | 195 <param name="aln_method" value="bowtie"/> |