Hello,
I've cloned and obtained a local Galaxy instance. I've followed the initial suggested steps (https://galaxyproject.org/admin/get-galaxy/) and have already installed tools from the shed, added references and created their indexes, etc. Everything went well and had no issue until this point. However I wanted to add a new tool that I can't find on the tool shed and so I've followed the steps from here: https://galaxyproject.org/admin/tools/add-tool-tutorial/. Initially, I wrote the tool definition xml file by hand and after adding it on the tool_config.xml it never showed on galaxy. I figured that the xml was invalid and tried to get it through Planemo. The xml outputted works perfectly on galaxy but I can't find on Planemo's documentation how to specify the input parameters characteristics so I did them by hand. By changing the xml file it stopped showing on galaxy but by changing it back to the original state it works again.
This is the xml file by planemo:
<tool id="vardict" name="VarDict" version="21.07.2018">
<description>Variant caller</description>
<requirements>
</requirements>
<command detect_errors="exit_code"><![CDATA[
vardict -G "$input1" -f "$input3" -b "$input2" -F 0 -c 1 -S 2 -E 3 -g 4 "$input4" | teststrandbias.R | var2vcf_valid.pl -f "$input3" -A > "$output1"
]]></command>
<inputs>
<param type="data" name="input1" format="fasta" />
<param type="data" name="input2" format="bam" />
<param type="data" name="input3" format="" />
<param type="data" name="input4" format="bed" />
</inputs>
<outputs>
<data name="output1" format="vcf" />
</outputs>
<help><![CDATA[
/home/lucia/galaxy/tools/vardict/vardict [-n name_reg] [-b bam] [-c chr] [-S start] [-E end] [-s seg_starts] [-e seg_ends] [-x #_nu] [-g gene] [-f freq] [-r #_reads] [-B #_reads] region_info
VarDict is a variant calling program for SNV, MNV, indels (<120 bp default, but can be set using -I option), and complex variants. It accepts any BAM format, either
from DNA-seq or RNA-seq. There are several distinct features over other variant callers. First, it can perform local
realignment over indels on the fly for more accurate allele frequencies of indels. Second, it rescues softly clipped reads
to identify indels not present in the alignments or support existing indels. Third, when given the PCR amplicon information,
it will perform amplicon-based variant calling and filter out variants that show amplicon bias, a common false positive in PCR
based targeted deep sequencing. Forth, it has very efficient memory management and memory usage is linear to the region of
interest, not the depth. Five, it can handle ultra-deep sequencing and the performance is only linear to the depth. It has
been tested on depth over 2M reads. Finally, it has a build-in capability to perform paired sample analysis, intended for
somatic mutation identification, comparing DNA-seq and RNA-seq, or resistant vs sensitive in cancer research. By default,
the region_info is an entry of refGene.txt from IGV, but can be any region or bed files.
(...)
]]></help>
<citations>
<citation type="doi">10.1093/nar/gkw227</citation>
<citation type="bibtex">
@misc{githubVarDict, author = {LastTODO, FirstTODO}, year = {TODO}, title = {VarDict}, publisher = {GitHub}, journal = {GitHub repository}, url = {https://github.com/AstraZeneca-NGS/VarDict}, }</citation> </citations> </tool>
I'd like to change the inputs to this:
<param type="data_meta" name="Reference" format="fasta" />
<param type="data" name="BAM file" format="bam" />
<param type="integer" value="0.005" name="Frequency" />
<param type="data" name="BED file" format="bed" />
Am I doing something wrong? Please let me know!
