comparison sr_bowtie_dataset_annotation.xml @ 8:3519c2de7fac draft

"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit e62066428e669516e024d081933ee8c7f953ba1b"

7:3bddd7ab96e3

<tool id="sr_bowtie_dataset_annotation" name="Annotate smRNA dataset" version="2.5.0">
  <description>by iterative alignments with sRbowtie</description>
  <requirements>
        <requirement type="package" version="1.3.1">bowtie</requirement>
        <requirement type="package" version="1.7.1">r-optparse</requirement>
        <requirement type="package" version="3.3.5">r-ggplot2</requirement>

                rm tmp_class_matched.fa &&
            #end for
            remaining=\$(( \$(wc -l < class_unmatched.fa)/2)) &&
            echo -e "$sample\tNot classified\t\${remaining}\t\${genome_aligned}" >> $output &&
        #end for
        
        
        Rscript $__tool_directory__/barplot.r --input $output --barplot $barplot
        ]]></command>
  <inputs>
    <param name="input" type="data" multiple="True" format="fasta,fastq" label="Input file: reads clipped from their adapter" help="Only with clipped, raw fasta or fastq files"/>
    <param name="mismatches" type="select" label="Number of mismatches allowed" help="specify the number of mismatches allowed during alignments">
        <option value="0">0</option>

        <param name="ownFile" type="data" format="fasta" label="Select a fasta file, to serve as index reference" />
    </repeat>
<!-- End of other bowtie index selections -->
   </inputs>
   <outputs>
       <data format="tabular" name="output" label="Cascade Annotation Analysis">
           <actions>
               <action name="column_names" type="metadata" default="Sample,Reference Index,Number of reads, Total reads" />
           </actions>
        </data>

            <param name="ownFile" value ="2L-tail.fa" ftype="fasta" />
            <param name="AdditionalQueries_0|ownFile" value="dme_miR21_hairpin.fa" ftype="fasta" />
            <param name="AdditionalQueries_1|ownFile" value="Ensembl_transposon_set.fa" ftype="fasta" />
            <output name="output" ftype="tabular" file="sample1_output.tab" />
            <output name="barplot" ftype="pdf" file="sample1_output.pdf" compare="sim_size" delta="500"/>
        </test>
        <test>
            <param name="input" value ="sample.fastq" ftype="fastq" />
            <param name="genomeSource" value="history" />
            <param name="ownFile" value ="2L-tail.fa" ftype="fasta" />
            <param name="AdditionalQueries_0|ownFile" value="dme_miR21_hairpin.fa" ftype="fasta" />
            <param name="AdditionalQueries_1|ownFile" value="Ensembl_transposon_set.fa" ftype="fasta" />
            <output name="output" ftype="tabular" file="sample_output.tab" />
            <output name="barplot" ftype="pdf" file="sample_output.pdf" compare="sim_size" delta="500"/>
        </test>
        <test>
            <param name="input" value ="sample5.fa,sample4.fa,sample3.fa,sample2.fa,sample1.fa" ftype="fasta" />
            <param name="genomeSource" value="history" />
            <param name="ownFile" value ="2L-tail.fa" ftype="fasta" />
            <param name="AdditionalQueries_0|ownFile" value="dme_miR21_hairpin.fa" ftype="fasta" />
            <param name="AdditionalQueries_1|ownFile" value="Ensembl_transposon_set.fa" ftype="fasta" />
            <output name="output" ftype="tabular" file="multisample5_output.tab" />
            <output name="barplot" ftype="pdf" file="multisample5_output.pdf" compare="sim_size" delta="500" />
        </test>
    </tests>
  <help>

**Introduction**

-----

**OUTPUTS**

**Annotation table in a tabular format**

  </help>
</tool>

8:3519c2de7fac

<tool id="sr_bowtie_dataset_annotation" name="Annotate smRNA dataset" version="2.6">
  <description>by iterative alignments with sRbowtie</description>
  <requirements>
        <requirement type="package" version="1.3.1">bowtie</requirement>
        <requirement type="package" version="1.7.1">r-optparse</requirement>
        <requirement type="package" version="3.3.5">r-ggplot2</requirement>

                rm tmp_class_matched.fa &&
            #end for
            remaining=\$(( \$(wc -l < class_unmatched.fa)/2)) &&
            echo -e "$sample\tNot classified\t\${remaining}\t\${genome_aligned}" >> $output &&
        #end for
        Rscript $__tool_directory__/barplot.r --input $output --barplot $barplot
        #if $format == '-q':
            && mv class_unmatched.fa class_unmatched.fastq
            && sed -n '1~4s/^@/>/p;2~4p' class_unmatched.fastq > class_unmatched.fa
        #end if
        ]]></command>
  <inputs>
    <param name="input" type="data" multiple="True" format="fasta,fastq" label="Input file: reads clipped from their adapter" help="Only with clipped, raw fasta or fastq files"/>
    <param name="mismatches" type="select" label="Number of mismatches allowed" help="specify the number of mismatches allowed during alignments">
        <option value="0">0</option>

        <param name="ownFile" type="data" format="fasta" label="Select a fasta file, to serve as index reference" />
    </repeat>
<!-- End of other bowtie index selections -->
   </inputs>
   <outputs>
       <data format="fasta" name="unmatched" label="Annotate smRNAs: Unmatched reads" from_work_dir="class_unmatched.fa" />
       <data format="tabular" name="output" label="Cascade Annotation Analysis">
           <actions>
               <action name="column_names" type="metadata" default="Sample,Reference Index,Number of reads, Total reads" />
           </actions>
        </data>

            <param name="ownFile" value ="2L-tail.fa" ftype="fasta" />
            <param name="AdditionalQueries_0|ownFile" value="dme_miR21_hairpin.fa" ftype="fasta" />
            <param name="AdditionalQueries_1|ownFile" value="Ensembl_transposon_set.fa" ftype="fasta" />
            <output name="output" ftype="tabular" file="sample1_output.tab" />
            <output name="barplot" ftype="pdf" file="sample1_output.pdf" compare="sim_size" delta="500"/>
            <output name="unmatched" ftype="fasta" file="unmatched_1.fa" />
        </test>
        <test>
            <param name="input" value ="sample.fastq" ftype="fastq" />
            <param name="genomeSource" value="history" />
            <param name="ownFile" value ="2L-tail.fa" ftype="fasta" />
            <param name="AdditionalQueries_0|ownFile" value="dme_miR21_hairpin.fa" ftype="fasta" />
            <param name="AdditionalQueries_1|ownFile" value="Ensembl_transposon_set.fa" ftype="fasta" />
            <output name="output" ftype="tabular" file="sample_output.tab" />
            <output name="barplot" ftype="pdf" file="sample_output.pdf" compare="sim_size" delta="500"/>
            <output name="unmatched" ftype="fasta" file="unmatched_2.fa" />
        </test>
        <test>
            <param name="input" value ="sample5.fa,sample4.fa,sample3.fa,sample2.fa,sample1.fa" ftype="fasta" />
            <param name="genomeSource" value="history" />
            <param name="ownFile" value ="2L-tail.fa" ftype="fasta" />
            <param name="AdditionalQueries_0|ownFile" value="dme_miR21_hairpin.fa" ftype="fasta" />
            <param name="AdditionalQueries_1|ownFile" value="Ensembl_transposon_set.fa" ftype="fasta" />
            <output name="output" ftype="tabular" file="multisample5_output.tab" />
            <output name="barplot" ftype="pdf" file="multisample5_output.pdf" compare="sim_size" delta="500" />
            <output name="unmatched" ftype="fasta" file="unmatched_3.fa" />
        </test>
    </tests>
  <help>

**Introduction**

-----

**OUTPUTS**

**- Annotation table in a tabular format**

**- Pie Charts of class abundances**

**- Unmatched reads in fasta format**

  </help>

  <citations>
    <citation type="doi">10.1038/nature11416</citation>
  </citations>

</tool>