changeset 0:963905bcb754 draft

planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mirdeep2.Rmd	Tue Aug 08 13:14:41 2017 -0400
@@ -0,0 +1,146 @@
+---
+title: 'Mirdeep2'
+output:
+    html_document:
+      number_sections: true
+      toc: true
+      theme: cosmo
+      highlight: tango
+---
+
+```{r setup, include=FALSE, warning=FALSE, message=FALSE}
+knitr::opts_chunk$set(
+  echo = ECHO
+)
+```
+
+# Job command line
+
+```{r 'build PATH', echo=FALSE}
+# set PATH environment.
+PATH = system('pwd', intern = TRUE) %>% 
+  (function(x) {
+    paste0('/home/galaxy/mirdeep2/bin:', x)
+  }) %>%
+    (function(x) {
+    paste0('/home/galaxy/mirdeep2_patch:', x)
+  }) %>%
+  paste0(':$PATH') 
+```
+
+## Build job command line.
+
+```{r 'build command line'}
+# change directory to OUTPUT DIR
+command_line = paste0('cd OUTPUT_DIR &&') %>%
+  # PATH and other environment variables
+  paste0('export PATH=', PATH, ' && ') %>%
+  (function(x) {
+    paste0(x, 'export PERL_MB_OPT="--install_base /home/galaxy/perl5" &&
+           export PERL_MM_OPT="INSTALL_BASE=/home/galaxy/perl5" &&
+           export PERL5LIB=/home/galaxy/mirdeep2/lib/perl5 && ')
+  }) %>%
+  # link collapsed reads and reads mapping files
+  (function(x) {
+    paste0(x, 'ln -s COLLAPSED_READS reads_collapsed.fa && ')
+  }) %>%
+  (function(x) {
+    paste0(x, 'ln -s READS_MAPPING reads_collapsed_vs_genome.arf && ')
+  }) %>%
+  paste0(' miRDeep2.pl ') %>%
+  # collapsed reads
+  (function(x) {
+    paste0(x, ' reads_collapsed.fa ')
+  }) %>%
+  # reference genome
+  (function(x) {
+    paste0(x, ' REFERENCE_GENOME ')
+  }) %>%
+  # reads mapping
+  (function(x) {
+    paste0(x, ' reads_collapsed_vs_genome.arf ')
+  }) %>%
+  # mature miRNA for this species
+  (function(x) {
+    if('SPECIES_MATURE_MIRNA' == 'None') {
+      paste0(x, tolower('SPECIES_MATURE_MIRNA'), ' ')
+    } else {
+      paste0(x, ' SPECIES_MATURE_MIRNA ')
+    }
+  }) %>%
+  # mature miRNA from related species
+  (function(x) {
+    if('SPECIES_RELATED_MATURE_MIRNA' == 'None') {
+      paste0(x, tolower('SPECIES_RELATED_MATURE_MIRNA'), ' ')
+    } else {
+      paste0(x, 'SPECIES_RELATED_MATURE_MIRNA ')
+    }
+  }) %>%
+  # precursor sequences
+  (function(x) {
+    if('PRECURSOR_SEQUENCES' == 'None') {
+      paste0(x, tolower('PRECURSOR_SEQUENCES'), ' ')
+    } else {
+      paste0(x, 'PRECURSOR_SEQUENCES ')
+    }
+  }) %>%
+  # min read stack height
+  (function(x) {
+    ifelse('MIN_READ_STACK_HEIGHT' == 'TRUE', x, paste0(x, ' -a MIN_READ_STACK_HEIGHT '))
+  }) %>%
+  # min score cutoff
+  (function(x) {
+    paste0(x, '-b MIN_SCORE_CUTOFF ')
+  }) %>%
+  # disable randfold analysis
+  (function(x) {
+    ifelse(RANDFOLD_ANALYSIS, paste0(x, '-c '), x)
+  }) %>%
+  # max precursors number
+  (function(x) {
+    paste0(x, ' -g MAX_PRECURSOR_NUMBER ')
+  }) %>%
+  # species
+  (function(x) {
+    ifelse('SPECIES' == 'all', x, paste0(x, ' -t SPECIES '))
+  }) %>%
+  # switch
+  (function(x) {
+    ifelse(SWITCH, x, paste0(x, ' -P '))
+  }) %>%
+  # write stdout to reprot.log
+  (function(x) {
+    paste0(x, ' >report.log 2>&1 ')
+  })
+  
+command_line
+
+## run job
+system(command_line)
+```
+
+## Results
+
+```{r echo=TRUE}
+system('cp OUTPUT_DIR/result*.html result.html')
+system('cp OUTPUT_DIR/result*.csv result.csv')
+system('cp OUTPUT_DIR/report.log report.log')
+system('mv OUTPUT_DIR/pdfs_* OUTPUT_DIR/pdfs')
+
+## check if OUTPUT DIR has results that we want.
+system('ls OUTPUT_DIR', intern = TRUE)
+```
+
+### PDF files
+
+```{r echo=TRUE}
+pdf_report_list = list()
+pdf_files = list.files('OUTPUT_DIR/pdfs', pattern = '.*pdf')
+pdf_files
+for (i in pdf_files) {
+  # note that the root directory is OUTPUT_DIR, all the file links should be a relative path to the root directory!
+  pdf_report_list[[i]] = tags$li(tags$a(href=paste0('pdfs/', i), i))
+}
+tags$ul(pdf_report_list)
+```
+

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mirdeep2.xml	Tue Aug 08 13:14:41 2017 -0400
@@ -0,0 +1,181 @@
+<tool id="mirdeep2" name="mirdeep2" version="1.0.0">
+    <requirements>
+        <requirement type="package" version="2.0.0.8">mirdeep2</requirement>
+        <requirement type="package" version="1.20.0">r-getopt</requirement>
+        <requirement type="package" version="1.2">r-rmarkdown</requirement>
+        <requirement type="package" version="1.8.4">r-plyr</requirement>
+        <requirement type="package" version="0.5.0">r-dplyr</requirement>
+        <requirement type="package" version="0.3.5">r-htmltools</requirement>
+    </requirements>
+    <description>
+        miRNA identification
+    </description>
+    <stdio>
+        <regex match="Execution halted"
+               source="both"
+               level="fatal"
+               description="Execution halted." />
+        <regex match="Error in"
+               source="both"
+               level="fatal"
+               description="An undefined error occured, please check your intput carefully and contact your administrator." />
+        <regex match="Fatal error"
+               source="both"
+               level="fatal"
+               description="An undefined error occured, please check your intput carefully and contact your administrator." />
+    </stdio>
+    <command>
+        <![CDATA[
+        ## Add tools to PATH
+        export PATH=/opt/R-3.2.5/bin:\$PATH &&
+
+        Rscript '${__tool_directory__}/mirdeep2_render.R'
+
+            ## 1. input data
+            -e $echo
+            -a $collapsed_reads
+		    -b $reference_genome
+		    -c $reads_mapping
+
+            ## 2. output report and report site directory
+		    -o $mirdeep2_site
+		    -d $mirdeep2_site.files_path
+		    -r $csv_result
+		    -t $html_result
+		    -u $report_log
+
+		    ## other paramters
+
+		    -f $species_mature_mirna
+		    -g $related_species_mature_mirna
+		    -h $precursor_sequences
+		    -j $min_read_stack_height
+		    -k $min_score_cutoff
+		    -l $randfold_analysis
+		    -m $max_precursor_number
+		    -n $species
+		    -q $switch
+
+		    ## 3. Rmd templates sitting in the tool directory
+
+                ## other Rmd body template files
+		        -p  '${__tool_directory__}/mirdeep2.Rmd'
+
+
+        ]]>
+    </command>
+    <inputs>
+        <param name="collapsed_reads" type="data" format="fasta" multiple="False" optional="False"
+               label="Read input file" help="Reads in fastq or fasta format"/>
+        <param name="reference_genome" type="data" format="fasta" multiple="False" optional="False"
+               label="Reference genome from history"
+               help="Reference genome in fasta format"/>
+        <param name="reads_mapping" type="data" format="tabular" multiple="False" optional="False"
+               label="reads mappings" help="reads mappings in arf format"/>
+        <param name="species_mature_mirna" type="data" format="fasta" multiple="False" optional="True"
+               label="miRBase mature miRNA for this species"
+               help="mature miRNA in fasta format"/>
+        <param name="related_species_mature_mirna" type="data" format="fasta" multiple="False" optional="TRUE"
+               label="miRBase mature miRNA from related species"
+               help="mature miRNA in fasta format"/>
+        <param name="precursor_sequences" type="data" format="fasta" multiple="False" optional="TRUE"
+               label="precursor sequences" help="miRBase miRNA precursor sequences in fasta format"/>
+        <param name="min_read_stack_height" type="integer" argument="-a" optional="True"
+               label="minimum read stack height"
+               help="minimum read stack height that triggers analysis. Using this option disables
+               automatic estimation of the optimal value."/>
+        <param name="min_score_cutoff" type="integer" value="0" argument="-b" label="minimum score cut-off"
+               help="minimum score cut-off for predicted novel miRNAs to be displayed in the overview
+              table. This score cut-off is by default 0."/>
+        <param name="randfold_analysis" type="boolean" truevalue="TRUE" falsevalue="FALSE" argument="-c" checked="False"
+               label="randfold analysis" help="disable randfold analysis"/>
+        <param name="max_precursor_number" type="integer" value="50000" argument="-g" label="maximum number of precursors"
+               help="maximum number of precursors to analyze when automatic excision gearing is used.
+              default=50000, if set to -1 all precursors will be analyzed"/>
+        <param name="species" type="select" label="Search in species">
+            <option value="all">All species</option>
+            <option value="tni">tetraodon</option>
+            <option value="dps">d.pseudoobscura</option>
+            <option value="dya">d.yakuba</option>
+            <option value="ame">a.mellifera</option>
+            <option value="dmo">d.mojavensis</option>
+            <option value="cel">worm</option>
+            <option value="aga">a.gambiae</option>
+            <option value="cbr">c.briggsae</option>
+            <option value="cin">c.intestinalis</option>
+            <option value="mmu">mouse</option>
+            <option value="xtr">x.tropicalis</option>
+            <option value="eca">horse</option>
+            <option value="cfa">dog</option>
+            <option value="fru">fugu</option>
+            <option value="bta">cow</option>
+            <option value="der">d.erecta</option>
+            <option value="dgr">d.grimshawi</option>
+            <option value="gga">chicken</option>
+            <option value="spu">s.purpuratus</option>
+            <option value="bfl">lancelet</option>
+            <option value="ptr">chimp</option>
+            <option value="dse">d.sechellia</option>
+            <option value="dpe">d.persimilis</option>
+            <option value="dvi">d.virilis</option>
+            <option value="rno">rat</option>
+            <option value="dme">d.melanogaster</option>
+            <option value="lca">cat</option>
+            <option value="sja">c.japonica</option>
+            <option value="dan">d.ananassae</option>
+            <option value="hsa">human</option>
+            <option value="dsi">d.simulans</option>
+        </param>
+        <param name="switch" type="boolean" truevalue="TRUE" falsevalue="FALSE"
+               label="mature_ref_miRNAs contain miRBase v18 identifiers?"
+               help="use this switch if mature_ref_miRNAs contain miRBase v18 identifiers (5p and 3p) instead of previous ids from v17"/>
+
+
+        <param name="echo" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Display analysis code in report?" />
+    </inputs>
+    <outputs>
+        <data format="html" name="mirdeep2_site" label="mirdeep2 miRNA identification" />
+        <data name="csv_result" format="csv" label="miRNA in csv format" />
+        <data name="html_result" format="html" label="miRNA in html format" from_work_dir="result.html"/>
+        <data name="report_log" format="txt" label="report log" from_work_dir="result.csv"/>
+    </outputs>
+    <citations>
+        @article{friedlander2011mirdeep2,
+        title={miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades},
+        author={Friedl{\"a}nder, Marc R and Mackowiak, Sebastian D and Li, Na and Chen, Wei and Rajewsky, Nikolaus},
+        journal={Nucleic acids research},
+        volume={40},
+        number={1},
+        pages={37--52},
+        year={2011},
+        publisher={Oxford University Press}
+        }
+        <citation type="bibtex">
+            @article{allaire2016rmarkdown,
+            title={rmarkdown: Dynamic Documents for R, 2016},
+            author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff and Wickham, Hadley and Atkins, Aron and Hyndman, Rob},
+            journal={R package version 0.9},
+            volume={6},
+            year={2016}
+            }
+        </citation>
+        <citation type="bibtex">
+            @book{xie2015dynamic,
+            title={Dynamic Documents with R and knitr},
+            author={Xie, Yihui},
+            volume={29},
+            year={2015},
+            publisher={CRC Press}
+            }
+        </citation>
+        <citation type="bibtex">
+            @book{xie2015dynamic,
+            title={Dynamic Documents with R and knitr},
+            author={Xie, Yihui},
+            volume={29},
+            year={2015},
+            publisher={CRC Press}
+            }
+        </citation>
+    </citations>
+</tool>
\ No newline at end of file

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mirdeep2_mapper.Rmd	Tue Aug 08 13:14:41 2017 -0400
@@ -0,0 +1,96 @@
+---
+title: 'Mirdeep2 Mapper'
+output:
+    html_document:
+      number_sections: true
+      toc: true
+      theme: cosmo
+      highlight: tango
+---
+
+```{r setup, include=FALSE, warning=FALSE, message=FALSE}
+knitr::opts_chunk$set(
+    echo = ECHO
+)
+```
+
+# Job command line
+
+## View arguments from command line.
+
+```{r 'view arguments'}
+str(opt)
+```
+
+```{r 'build PATH', echo=FALSE}
+# set PATH environment.
+PATH = system('pwd', intern = TRUE) %>% 
+  (function(x) {
+    paste0('/home/galaxy/mirdeep2/bin:', x)
+  }) %>%
+  paste0(':$PATH')
+```
+
+
+## Build job command line.
+
+```{r 'build command line'}
+command_line = paste0('export PATH=', PATH, ' && ') %>%
+  # index reference genome
+  paste0(' bowtie-build REFERENCE_GENOME ref_genome &&') %>%
+  paste0(' mapper.pl ') %>%
+  # reads
+  (function(x) {
+    paste0(x, 'FASTQ_READS -c ')
+  }) %>%
+  # reference genome
+  (function(x) {
+    paste0(x, '-p ref_genome ')
+  }) %>%
+  # # parse to fasta
+  # (function(x) {
+  #   ifelse(PARSE_TO_FASTA, paste0(x, '-h '), x)
+  # }) %>%
+  # clean entries
+  (function(x) {
+    ifelse(CLEAN_ENTRIES, paste0(x, '-j '), x)
+  }) %>%
+  # clip 3 adapter
+  (function(x) {
+    ifelse('CLIP_3_ADAPTER' == '', x, paste0(x, '-k CLIP_3_ADAPTER '))
+  }) %>%
+  # discard shorter reads
+  (function(x) {
+    paste0(x, '-l DISCARD_SHORTER_READS ')
+  }) %>%
+  # collapse reads
+  (function(x) {
+    # ifelse(COLLAPSE_READS, paste0(x, '-m '), x)
+    paste0(x, '-m ')
+  }) %>%
+  # map with one mismatch
+  (function(x) {
+    ifelse(MAP_WITH_ONE_MISMATCH, paste0(x, '-q '), x)
+  }) %>%
+  # map up to position
+  (function(x) {
+    paste0(x, '-r MAP_UP_TO_POSITION ')
+  }) %>%
+  # overwrite existing files(-n), outputs
+  (function(x) {
+    paste0(x, '-s reads_collapsed.fa -t reads_collapsed_vs_genome.arf -v -n ')
+  }) %>%
+  # write stdout to reprot.log
+  (function(x) {
+    paste0(x, ' 2>report.log')
+  })
+command_line
+```
+
+## Run command line
+
+```{r}
+system(command_line)
+```
+
+

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mirdeep2_mapper.xml	Tue Aug 08 13:14:41 2017 -0400
@@ -0,0 +1,135 @@
+<tool id="mirdeep2_mapper_site" name="mirdeep2_mapper" version="1.0.0">
+    <requirements>
+        <requirement type="package" version="2.0.0.8">mirdeep2</requirement>
+        <requirement type="package" version="1.20.0">r-getopt</requirement>
+        <requirement type="package" version="1.2">r-rmarkdown</requirement>
+        <requirement type="package" version="1.8.4">r-plyr</requirement>
+        <requirement type="package" version="0.5.0">r-dplyr</requirement>
+        <requirement type="package" version="0.3.5">r-htmltools</requirement>
+    </requirements>
+    <description>
+        Mapping reads to genome
+    </description>
+    <stdio>
+        <regex match="Execution halted"
+               source="both"
+               level="fatal"
+               description="Execution halted." />
+        <regex match="Error in"
+               source="both"
+               level="fatal"
+               description="An undefined error occured, please check your intput carefully and contact your administrator." />
+        <regex match="Fatal error"
+               source="both"
+               level="fatal"
+               description="An undefined error occured, please check your intput carefully and contact your administrator." />
+    </stdio>
+    <command>
+        <![CDATA[
+        ## Add tools to PATH
+        export PATH=/opt/R-3.2.5/bin:\$PATH &&
+
+        Rscript '${__tool_directory__}/mirdeep2_mapper_render.R'
+
+            ## 1. input data
+            -r $reads
+            -g $reference_genome
+            -e $echo
+
+            ## 2. output report and report site directory
+		    -o $mirdeep2_mapper_site
+		    -d $mirdeep2_mapper_site.files_path
+		    -m $reads_collapsed
+		    -n $reads_collapsed_vs_genome
+		    -t $report_log
+
+		    ## other parameters
+		    -b $parse_to_fasta
+		    -c $clean_entries
+		    -f $clip_3_adapter
+		    -h $discard_shorter_reads
+		    -j $collapse_reads_or_not
+		    -k $map_with_one_mismatch
+		    -l $map_up_to_position
+
+
+		    ## 3. Rmd templates sitting in the tool directory
+
+                ## other Rmd body template files
+		        -p '${__tool_directory__}/mirdeep2_mapper.Rmd'
+
+
+
+        ]]>
+    </command>
+    <inputs>
+        <param name="reads" type="data" format="fastq,fasta" multiple="False" optional="False"
+               label="Read input file" help="Reads in fastq or fasta format"/>
+        <param name="reference_genome" type="data" format="fasta" multiple="false" optional="False" argument="-p"
+               label="Reference genome from history" />
+
+        <param name="parse_to_fasta" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" argument="-h"
+               optional="True" label="Parse to fasta format" />
+        <param name="clean_entries" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" argument="-j"
+               optional="True" label="Remove reads with non-canonical letters"
+               help="remove all entries that have a sequence that contains letters other than a,c,g,t,u,n,A,C,G,T,U,N" />
+        <param name="clip_3_adapter" type="text" argument="-k" value="" optional="true" label="Clip 3' adapter sequence (optional)"
+               help="Enter an adapter sequence"/>
+        <param name="discard_shorter_reads" type="integer" min="0" value="18" argument="-l"
+               label="Discard reads shorter than int nts" />
+        <param name="collapse_reads_or_not" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" argument="-m"
+               label="Collapse reads" />
+        <param name="map_with_one_mismatch" type="boolean" truevalue="TRUE" falsevalue="FALSE" argument="-q"
+               label="Map with one mismatch"
+               help="map with one mismatch in the seed (mapping takes longer)"/>
+        <param name="map_up_to_position" type="integer" min="1" value="5" label="Map up to int nts" argument="-r"
+               help="A read is allowed to map up to this number of positions in the genome. Default is 5"/>
+
+        <param name="echo" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Display analysis code in report?" />
+    </inputs>
+    <outputs>
+        <data name="mirdeep2_mapper_site" format="html" label="mirdeep2_mapper site" />
+        <data name="reads_collapsed" format="fasta" label="reads_collapsed" />
+        <data name="reads_collapsed_vs_genome" format="tabular" label="reads_collapsed_vs_ref_genome" />
+        <data name="report_log" format="txt" label="report log"/>
+    </outputs>
+    <citations>
+        @article{friedlander2011mirdeep2,
+        title={miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades},
+        author={Friedl{\"a}nder, Marc R and Mackowiak, Sebastian D and Li, Na and Chen, Wei and Rajewsky, Nikolaus},
+        journal={Nucleic acids research},
+        volume={40},
+        number={1},
+        pages={37--52},
+        year={2011},
+        publisher={Oxford University Press}
+        }
+        <citation type="bibtex">
+            @article{allaire2016rmarkdown,
+            title={rmarkdown: Dynamic Documents for R, 2016},
+            author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff and Wickham, Hadley and Atkins, Aron and Hyndman, Rob},
+            journal={R package version 0.9},
+            volume={6},
+            year={2016}
+            }
+        </citation>
+        <citation type="bibtex">
+            @book{xie2015dynamic,
+            title={Dynamic Documents with R and knitr},
+            author={Xie, Yihui},
+            volume={29},
+            year={2015},
+            publisher={CRC Press}
+            }
+        </citation>
+        <citation type="bibtex">
+            @book{xie2015dynamic,
+            title={Dynamic Documents with R and knitr},
+            author={Xie, Yihui},
+            volume={29},
+            year={2015},
+            publisher={CRC Press}
+            }
+        </citation>
+    </citations>
+</tool>
\ No newline at end of file

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mirdeep2_mapper_render.R	Tue Aug 08 13:14:41 2017 -0400
@@ -0,0 +1,153 @@
+##======= Handle arguments from command line ========
+# setup R error handline to go to stderr
+options(show.error.messages=FALSE,
+        error=function(){
+          cat(geterrmessage(), file=stderr())
+          quit("no", 1, F)
+        })
+
+# we need that to not crash galaxy with an UTF8 error on German LC settings.
+loc = Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
+
+# suppress warning
+options(warn = -1)
+
+options(stringsAsFactors=FALSE, useFancyQuotes=FALSE)
+args = commandArgs(trailingOnly=TRUE)
+
+suppressPackageStartupMessages({
+  library(getopt)
+  library(tools)
+})
+
+# column 1: the long flag name
+# column 2: the short flag alias. A SINGLE character string
+# column 3: argument mask
+#           0: no argument
+#           1: argument required
+#           2: argument is optional
+# column 4: date type to which the flag's argument shall be cast.
+#           possible values: logical, integer, double, complex, character.
+spec_list=list()
+
+##------- 1. input data ---------------------
+spec_list$FASTQ_READS = c('reads', 'r', '1', 'character')
+spec_list$REFERENCE_GENOME = c('reference_genome', 'g', 1, 'character')
+spec_list$ECHO = c('echo', 'e', '1', 'character')
+
+##--------2. output report and report site directory --------------
+spec_list$OUTPUT_HTML = c('mirdeep2_mapper', 'o', '1', 'character')
+spec_list$OUTPUT_DIR = c('mirdeep2_mapper_dir', 'd', '1', 'character')
+spec_list$READS_COLLAPSED = c('reads_collapsed', 'm', '1', 'character')
+spec_list$READ_X_COLLAPSED_VS_GENOME = c('reads_collapsed_vs_genome', 'n', '1', 'character')
+spec_list$REPORT_LOG = c("report_log", 't', '1', 'character')
+
+##---------other parameters---------------
+spec_list$PARSE_TO_FASTA = c('parse_to_fasta', 'b', '1', 'character')
+spec_list$CLEAN_ENTRIES = c('clean_entries', 'c', '1', 'character')
+spec_list$CLIP_3_ADAPTER = c('clip_3_adapter', 'f', '2', 'character')
+spec_list$DISCARD_SHORTER_READS = c('discard_shorter_reads', 'h', '1', 'character')
+spec_list$COLLAPSE_READS_OR_NOT = c('collapse_reads_or_not', 'j', '1', 'character')
+spec_list$MAP_WITH_ONE_MISMATCH = c('map_with_one_mismatch', 'k', '1', 'character')
+spec_list$MAP_UP_TO_POSITION = c('map_up_to_position', 'l', '1', 'character')
+
+##--------3. Rmd templates sitting in the tool directory ----------
+
+## _site.yml and index.Rmd files
+spec_list$SITE_YML = c('site_yml', 's', 1, 'character')
+spec_list$INDEX_Rmd = c('index_rmd', 'i', 1, 'character')
+
+## other Rmd body template files
+spec_list$MIRDEEP2_MAPPER_RMD = c('mirdeep2_mapper_rmd', 'p', '1', 'character')
+
+
+
+##------------------------------------------------------------------
+
+spec = t(as.data.frame(spec_list))
+opt = getopt(spec)
+# arguments are accessed by long flag name (the first column in the spec matrix)
+#                        NOT by element name in the spec_list
+# example: opt$help, opt$expression_file
+##====== End of arguments handling ==========
+
+#------ Load libraries ---------
+library(rmarkdown)
+library(plyr)
+# library(stringr)
+library(dplyr)
+# library(highcharter)
+# library(DT)
+# library(reshape2)
+# library(plotly)
+# library(formattable)
+library(htmltools)
+
+
+#----- 1. create the report directory ------------------------
+paste0('mkdir -p ', opt$mirdeep2_mapper_dir) %>%
+  system()
+
+#----- 2. generate Rmd files with Rmd templates --------------
+#   a. templates without placeholder variables:
+#         copy templates from tool directory to the working directory.
+#   b. templates with placeholder variables:
+#         substitute variables with user input values and place them in the working directory.
+
+
+#----- mirdeep2_mapper.Rmd -----------------------
+readLines(opt$mirdeep2_mapper_rmd) %>%
+  (function(x) {
+    gsub('ECHO', opt$echo, x)
+  }) %>%
+  (function(x) {
+    gsub('FASTQ_READS', opt$reads, x)
+  }) %>% 
+  (function(x) {
+    gsub('REFERENCE_GENOME', opt$reference_genome, x)
+  }) %>%
+  (function(x) {
+    gsub('PARSE_TO_FASTA', opt$parse_to_fasta, x)
+  }) %>%
+  (function(x) {
+    gsub('CLEAN_ENTRIES', opt$clean_entries, x)
+  }) %>%
+  (function(x) {
+    gsub('CLIP_3_ADAPTER', opt$clip_3_adapter, x)
+  }) %>%
+  (function(x) {
+    gsub('DISCARD_SHORTER_READS', opt$discard_shorter_reads, x)
+  }) %>%
+  (function(x) {
+    gsub('COLLAPSE_READS', opt$collapse_reads, x)
+  }) %>%
+  (function(x) {
+    gsub('MAP_WITH_ONE_MISMATCH', opt$map_with_one_mismatch, x)
+  }) %>%
+  (function(x) {
+    gsub('MAP_UP_TO_POSITION', opt$map_up_to_position, x)
+  }) %>%
+  (function(x) {
+    gsub('OUTPUT_DIR', opt$mirdeep2_mapper_dir, x)
+  }) %>%
+  (function(x) {
+    fileConn = file('mirdeep2_mapper.Rmd')
+    writeLines(x, con=fileConn)
+    close(fileConn)
+  })
+
+
+#------ 3. render all Rmd files with render() --------
+render('mirdeep2_mapper.Rmd', output_file = opt$mirdeep2_mapper)
+
+
+#-------4. manipulate outputs -----------------------------
+#   a. copy non-site files
+file.copy('reads_collapsed.fa', opt$reads_collapsed, recursive=TRUE)
+file.copy('reads_collapsed_vs_genome.arf', opt$reads_collapsed_vs_genome, recursive=TRUE)
+file.copy('report.log', opt$report_log, recursive=TRUE)
+
+
+
+
+

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mirdeep2_render.R	Tue Aug 08 13:14:41 2017 -0400
@@ -0,0 +1,164 @@
+##======= Handle arguments from command line ========
+# setup R error handline to go to stderr
+options(show.error.messages=FALSE,
+error=function(){
+    cat(geterrmessage(), file=stderr())
+    quit("no", 1, F)
+})
+
+# we need that to not crash galaxy with an UTF8 error on German LC settings.
+loc = Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
+
+# suppress warning
+options(warn = -1)
+
+options(stringsAsFactors=FALSE, useFancyQuotes=FALSE)
+args = commandArgs(trailingOnly=TRUE)
+
+suppressPackageStartupMessages({
+    library(getopt)
+    library(tools)
+})
+
+# column 1: the long flag name
+# column 2: the short flag alias. A SINGLE character string
+# column 3: argument mask
+#           0: no argument
+#           1: argument required
+#           2: argument is optional
+# column 4: date type to which the flag's argument shall be cast.
+#           possible values: logical, integer, double, complex, character.
+spec_list=list()
+
+##------- 1. input data ---------------------
+spec_list$ECHO = c('echo', 'e', '1', 'character')
+spec_list$COLLASPED_READS = c('collapsed_reads', 'a', '1', 'character')
+spec_list$REFERENCE_GENOME = c('reference_genome', 'b', '1', 'character')
+spec_list$READS_MAPPING = c('reads_mapping', 'c', '1', 'character')
+
+##--------2. output report and report site directory --------------
+spec_list$OUTPUT_HTML = c('mirdeep2_html', 'o', '1', 'character')
+spec_list$OUTPUT_DIR = c('mirdeep2_output_dir', 'd', '1', 'character')
+spec_list$CSV_RESULT = c('csv_result', 'r', '1', 'character')
+spec_list$HTML_RESULT = c('html_result', 't', '1', 'character')
+spec_list$REPORT_LOG = c('report_log', 'u', '1', 'character')
+
+##---------other parameters---------
+spec_list$SPECIES_MATURE_MIRNA = c('species_mature_mirna', 'f', '2', 'character')
+spec_list$SPECIES_RELATED_MATURE_MIRRNA = c('related_species_mature_mirna', 'g', '2', 'character')
+spec_list$PRECURSOR_SEQUENCES = c('precursor_sequences', 'h', '2', 'character')
+spec_list$MIN_READ_STACK_HEIGHT = c('min_read_stack_height', 'j', '2', 'character')
+spec_list$MIN_SCORE_CUTOFF = c('min_score_cutoff', 'k',  '2', 'character')
+spec_list$RANDFOLD_ANALYSIS = c('randfold_analysis', 'l', '2', 'character')
+spec_list$MAX_PRECURSOR_NUMBER = c('max_precursor_number', 'm', '2', 'character')
+spec_list$SPECIES = c('species', 'n', '2', 'character')
+spec_list$SWITCH = c('switch', 'q', '2', 'character')
+
+##--------3. Rmd templates sitting in the tool directory ----------
+
+## _site.yml and index.Rmd files
+spec_list$SITE_YML = c('site_yml', 's', 1, 'character')
+spec_list$INDEX_Rmd = c('index_rmd', 'i', 1, 'character')
+
+## other Rmd body template files
+spec_list$MIRDEEP2_RMD = c('mirdeep2_rmd', 'p', '1', 'character')
+
+
+
+##------------------------------------------------------------------
+
+spec = t(as.data.frame(spec_list))
+opt = getopt(spec)
+# arguments are accessed by long flag name (the first column in the spec matrix)
+#                        NOT by element name in the spec_list
+# example: opt$help, opt$expression_file
+##====== End of arguments handling ==========
+
+#------ Load libraries ---------
+library(rmarkdown)
+library(plyr)
+# library(stringr)
+library(dplyr)
+# library(highcharter)
+# library(DT)
+# library(reshape2)
+# library(plotly)
+# library(formattable)
+library(htmltools)
+
+
+#----- 1. create the report directory ------------------------
+paste0('mkdir -p ', opt$mirdeep2_output_dir) %>%
+system()
+
+#----- 2. generate Rmd files with Rmd templates --------------
+#   a. templates without placeholder variables:
+#         copy templates from tool directory to the working directory.
+#   b. templates with placeholder variables:
+#         substitute variables with user input values and place them in the working directory.
+
+
+#----- mirdeep2.Rmd -----------------------
+readLines(opt$mirdeep2_rmd) %>%
+  (function(x) {
+    gsub('ECHO', opt$echo, x)
+  }) %>%
+  (function(x) {
+    gsub('COLLAPSED_READS', opt$collapsed_reads, x)
+  }) %>%
+  (function(x) {
+    gsub('REFERENCE_GENOME', opt$reference_genome, x)
+  }) %>%
+  (function(x) {
+    gsub('READS_MAPPING', opt$reads_mapping, x)
+  }) %>%
+  (function(x) {
+    gsub('SPECIES_MATURE_MIRNA', opt$species_mature_mirna, x)
+  }) %>%
+  (function(x) {
+    gsub('SPECIES_RELATED_MATURE_MIRNA', opt$related_species_mature_mirna, x)
+  }) %>%
+  (function(x) {
+    gsub('PRECURSOR_SEQUENCES', opt$precursor_sequences, x)
+  }) %>%
+  (function(x) {
+    gsub('MIN_READ_STACK_HEIGHT', opt$min_read_stack_height, x)
+  }) %>%
+  (function(x) {
+    gsub('MIN_SCORE_CUTOFF', opt$min_score_cutoff, x)
+  }) %>%
+  (function(x) {
+    gsub('RANDFOLD_ANALYSIS', opt$randfold_analysis, x)
+  }) %>%
+  (function(x) {
+    gsub('MAX_PRECURSOR_NUMBER', opt$max_precursor_number, x)
+  }) %>%
+  (function(x) {
+    gsub('SPECIES', opt$species, x)
+  }) %>%
+  (function(x) {
+    gsub('SWITCH', opt$switch, x)
+  }) %>%
+  (function(x) {
+    gsub('OUTPUT_DIR', opt$mirdeep2_output_dir, x)
+  }) %>%
+  (function(x) {
+    fileConn = file('mirdeep2.Rmd')
+    writeLines(x, con=fileConn)
+    close(fileConn)
+  })
+
+
+#------ 3. render all Rmd files with render() --------
+render('mirdeep2.Rmd',output_file = opt$mirdeep2_html)
+
+
+#-------4. manipulate outputs -----------------------------
+#   a. copy non-site files
+file.copy('result.csv', opt$csv_result, recursive=TRUE)
+file.copy('result.html', opt$html_result, recursive=TRUE)
+file.copy('report.log', opt$report_log, recursive=TRUE)
+
+
+
+