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Tool help updates.

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This commit is contained in:
Daniel Blankenberg
2011-11-14 13:26:29 -05:00
parent 5b19eed45e
commit 7c930f1c92
4 changed files with 17 additions and 1 deletions
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tools/filters/secure_hash_message_digest.xml
+6
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@@ -35,5 +35,11 @@
This tool outputs Secure Hashes / Message Digests of a dataset using the user selected algorithms.
------
**Citation**
If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
</help>
</tool>
tools/filters/wc_gnu.xml
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@@ -62,5 +62,11 @@ This tool outputs counts of specified attributes (lines, words, characters) of a
#lines words characters
7499 41376 624971
------
**Citation**
If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
</help>
</tool>
tools/peak_calling/ccat_wrapper.xml
+3 -1
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@@ -112,7 +112,7 @@ bootstrapPass ${options_type[ 'bootstrap_pass' ]}
<output name="output_top_file" file="peakcalling_ccat/3.0/ccat_test_top_out_1.interval.sorted.re_match" compare="re_match" sort="true" />
<output name="output_log_file" file="peakcalling_ccat/3.0/ccat_test_log_out_1.txt" />
</test>
<!-- Test below gives different results on different architectures,
<!-- Test below gives different answers on different architectures,
e.g.: x86_64 GNU/Linux gave an extra line (additional peak called) when compared to the version running on 10.6.0 Darwin i386
slidingWinSize was fixed to be 1000, default as per readme.txt
-->
@@ -140,6 +140,8 @@ View the original CCAT documentation: http://cmb.gis.a-star.edu.sg/ChIPSeq/paper
**Citation**
For the underlying tool, please cite `Xu H, Handoko L, Wei X, Ye C, Sheng J, Wei CL, Lin F, Sung WK. A signal-noise model for significance analysis of ChIP-seq with negative control. Bioinformatics. 2010 May 1;26(9):1199-204. &lt;http://www.ncbi.nlm.nih.gov/pubmed/20371496&gt;`_
If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
</help>
tools/peak_calling/macs_wrapper.xml
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@@ -231,6 +231,8 @@ View the original MACS documentation: http://liulab.dfci.harvard.edu/MACS/00READ
**Citation**
For the underlying tool, please cite `Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XS. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008;9(9):R137. &lt;http://www.ncbi.nlm.nih.gov/pubmed/18798982&gt;`_
If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
</help>